The manual tells you, but I found it to not be very specific. I just took mine out yesterday; took all day as I'm a novice at it. First, turn the fuel off, unclip the hose from the gas tank that connects to the sub-tank, take off the back exhaust, the panel on that side, the bracket that holds the sub-tank (so you can actually move it to a position to pull it out), the 3 bolts that hold the sub-tank, unclip the hose and connection from the sub-tank, then pull the whole thing out. Take care to have a funnel or something ready to get the gas that comes out. The actual pump was a pain, as the white thing that the pump inserts in to has clips. Also, hold that over a bucket or something when you finally get it open as gas comes out of it too. Again, this is what I experienced. I did take the tank off too, but I'm not sure you actually have to take the tank off. It is a pain that everything is so packed tightly on the bike.
My question is the filter on top. Does that have to be replaced or can I reuse that? I ordered a "Quantum Intank EFI Fuel Pump For Yamaha Stryker (XVS1300) 2010-2020" from the site and praying it fits and works, but I don't see a filter on it, which is why I was asking if the other can be reused?