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Discussion Starter #1 (Edited)
For my first trick... I mean post..... I'll be writing up a brief quick tip guide for the Power Commander V Autotune on a bike with the stock exhaust set up. This will include everything I could remember from the install that I wish I'd explicitly known before hand.

There are plenty of threads about which tuner is best for you, and a few threads about installing the Autotune on different exhaust systems, but there are no write-ups (that I could find, at least) for installing on the stock exhaust system.

Why install the Power Commander/Autotune combo on a bike with no exhaust or intake modifications, you ask?
I had X-amount I was willing to spend on mods to get started, and was a little nervous about running new exhaust without the tuner set up- I know it wouldn't destroy the bike, but I'm just more comfortable doing the mods in this order. BUT, this thread is not for discussing that issue.

I'll try to keep this BRIEF, not going to get too technical on all of it.

Remove the exhaust system, being careful not to strip out the three black bolts holding on the muffler. On my bike these were EXTREMELY tight, I burnt through two battery charges on an electric impact wrench, and finally got them after two hours (and one almost stripped head) by using an 8mm socket wrench attachment.
Horrible quality pictures, but showing the general area
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I have the forward extensions on my footpegs, which gave me room to remove the pipe for the front cylinder. If you do not have these extensions, you may need to loosen your right footpeg from the frame a little bit. I don't think it's absolutely necessary to remove this front pipe, but I found it gave me a lot more freedom when test fitting the rear y-pipe later on.

Do yourself a HUGE favor, wrap the exposed radiator and/or frame with tape, or a clean rag such as I did. You WILL bump this with the front exhaust pipe at least once, that I can promise you.
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Plan location for the wide-band O2 sensor, I put mine on the back side of the rear exhaust pipe, and drilled/cut a hole in the black shroud right behind it. YES, YOU NEED TO KEEP THE STOCK O2 SENSOR AS WELL. There are other threads explaining this.
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EFI bikes have similar enough O2 readings between the cylinders that having the wide-band O2 sensor on one of the pipes (as opposed to in a collector area or having one sensor on each pipe) does not make a huge difference. Your bike will not explode.

Mark the pipe where you want the bung welded in and either install it yourself, if you're so inclined, or take it to an exhaust shop. Some people had there's installed for ~$10, the shop I took mine to charged me $30. They have a skill that I do not, I don't mind paying extra for them to use that skill to my benefit.

When drilling the hole, I used a step drill that I found in my yard covered in rust, and that worked just fine for me. You may need to expand the hole toward the rear of the bike a bit with a dremel, box knife, or Carrie Fisher's coke nail from Return of the Jedi- it's probably available for sale online somewhere, she HAS to have cut it by now, right? Really any sharp object will do.

Test fit the y-pipe part of the exhaust with the black shroud in place and wide-band sensor installed hand-tight. Extend the hole in the shroud until you can easily install the y-pipe, including a little wiggle room, without cursing the Bike Gods or scratching/bending anything.

The wide-band sensor connector can run up to the reserve tank that's hidden behind the side cover. At the top of this picture you'll see it tucked in there, I used some extra velcro pads to attach it to the front of the reserve tank, and used a small zip-tie to hold the velcro to the connector, as it's an odd shape.
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The extra wire going to the autotune is just coiled up and zip-tied, then placed on top of the reserve tank, sitting loosely for now- I may make it more secure if I come across any problems with it in the future.

I cut the battery tray so I could comfortably fit the autotune and PCV in there without having to bend the wires to run them out. It may not look pretty, but it's under the seat, so whatever.
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This is fairly soft plastic so, again- drill, dremel, box knife, coke nail, you get it.

They provide a ring lug you can use to connect the black wire to the negative post of your battery, and some wire tap thingies you can use to connect the red wire to a switched 12v source.
The easiest 12v source I found was the tail light running wire. Locate the little black fuse box on the left side of the battery housing, press the tab so you can pull it out, and tap into the blue wire connected underneath.
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The autotune will now receive power whenever your ignition is in the on position.

Everything buttons up nicely, looks clean, and runs well.
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Plug in the supplied cable between the PCV and autotune.

Capt_Zoom has a detailed write up on proper use of the autotune here:http://www.yamahastarstryker.com/20-how-tos/854-how-use-pcv-autotune-create-good-map-reduce-backfiring.html

Good luck, if you have any questions, I will try to answer, but I'm just a moderately intelligent guy faking my way through things as I go along, and common sense is always the best guide.

Any suggestions about my bike, this install tip guide, or edits, please post and I will do my best to respond or edit.

Thanks!
 

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Thank you for the guide/tutorial on installing the Dynojet, but you might want to check your links to your images. No images are being shown with the tutorial

UPDATE((( PICTURES ARE NOW FIXED!))) Thank you Dgoss619
 

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Welcome! I can see your pics no problems here. Great you spent the time to do a write-up with pics!
I get that you wanted to get the tuner before exhaust and or intake upgrades. Like some of us, Myself included, just cannot afford to spend the $1300-1600 to do it all at once. For the cost of a programmer, auto tuner, welding work (which I think was unnecessary), but will give my reasoning in a moment. You could of had your ECU reprogrammed for $350 plus shipping and would of been much happier with the results, as this would of taken care of many more issues than just a lean fuel problem. Here is a link to the shop that does this-- http://www.ivansperformanceproducts.com/contact.htm

I have done a lot of reading up on Fuel programmers for our Strykers and also have talked with some about what is best for our application. For the power commander and it's auto tune module I see no mention of adding a separate O2 sensor, it states you are to use the factory one-and jumper the optimizer connections using the stock wiring harness. http://www.powercommander.com/downloads/22-042/install/pcv/engI22-042.03.pdf

Unless I've missed something and very well could be, as I have not installed that unit myself, you may have done more work than needed.
Here are a few links to read up on some are very long, but great reading.
http://www.yamahastarstryker.com/21-technical-discussion/34170-ecu-flash-need-volunteer.html

This one I have done myself with great success- http://www.yamahastarstryker.com/21-technical-discussion/45650-ecu-getting-into-factory-ecu-change-air-fuel-ratio-co-mode.html
 

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Discussion Starter #4 (Edited)
Mod, are the pictures working for you now? I think I had just finished fixing picture issues around the time you posted, I may have just missed you.

Slick, thanks for the response!
I had considered the ECU flash, and may do so in the future, as it does fix a few problems that I don't think the Power Commander V w/ autotune could fix, but I went with the programmer first because it allows for easier modifications later on. I haven't put too much research into Ivan's flash, but I will in the future when I have the spare cash.

The O2 optimizer does connect to the Power Commander V and utilizes the stock O2 sensor, you're correct on that. However, the Autotune requires the stock sensor, with optimizer, to remain to control the closed loop section of the fuel map, while a second sensor (wide-band O2 sensor) needs to be added for tuning purposes.

While the ECU flash would have been cheaper, and maybe even better in the short-term, the tuner combo I have allows me to switch out intake and exhaust all I want with little-to-no extra tuning work. If I'd gone with just the ECU flash, I'd still have to have a tuner (or another ECU flash) of some sort when I change intake or exhaust in the future.

The power commander and autotune also allow me to get a custom tune, made for my bike, my altitude and climate, my specific modifications, as opposed to downloading someone else's tune with similar exhaust-intake setup, and hoping my bike runs well with it.

Thanks for the input!
 

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While the ECU flash would have been cheaper, and maybe even better in the short-term, the tuner combo I have allows me to switch out intake and exhaust all I want with little-to-no extra tuning work. If I'd gone with just the ECU flash, I'd still have to have a tuner (or another ECU flash) of some sort when I change intake or exhaust in the future.
The Flash from Ivan is a flash, a flash, a flash, same for everyone no matter what setup they have on their Stryker. Does 95% tune for everyone regardless of their mods. The PCV does the last 5%.
 

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Ivan's tune covers all exhaust/intake options. The best thing about ivans tune to me is the removal of the fuel cutoff, that cause most all the issues with this bike and can't be fixed unless you flash. It can be masked to a point, but only way to remove that is to remove it from the factory program. I have also chosen to add the fuel programmer (PCFC) to get the full 100% optimized tune. I will install that once I get the pipes for it. I guess it's all what some prefer, I rode my bike with out a tune for two years and while at hi-way speeds she ran like a rapped ape, but city driving the most horrible experience, chugging, bucking, poor throttle response, popping through the intake. While I was able to cure the popping and gain a little better response with the CO mode mod, I hated driving in first and second gear, and it felt worse doing it 2-up.

My ECU should be here tomorrow and I can't wait to feel the difference, I may actually enjoy doing the speed limit....... oh **** no who am I kidding it's 90 or nothing!
 

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...My ECU should be here tomorrow and I can't wait to feel the difference, I may actually enjoy doing the speed limit....... oh **** no who am I kidding it's 90 or nothing!
The speed limit is 85 in some parts of Texas. :D 75 dam near everywhere.
 

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So what is the issue say removing the stock O2 sensor and optimizer and screwing in the WB sensor in place and running directly to the Autotune?
 
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