Haven't noticed any more engine heat than any other liquid cooled motorcycle I've owned. You could try an exhaust wrap, that would force more heat out the tail of the exhaust. Engines run anywhere from 140 - 220 degrees, so depending on the design you'll feel more or less heat. On full fairing bikes the heat is typically blocked well where as naked bikes like the Stryker heat simply goes where it can. You can't compare two different bikes when it comes to heat dissipation. Only time I notice any heat is at a stop when the fan is running. Not a whole lot can be done about it. Wouldn't worry too much about it unless the engine temp warning light illuminates. If the heat bothers you that much I'd recommend trying an exhaust wrap / full exhaust. Removing the cats helps exhaust flow and reduces heat build up.
Air intake might make some difference while moving, but I wouldn't expect much of a difference.
