Hot starts can be a multitude of things. First of all, do you have a maintenance free battery? The wet cell batteries are known for eventually giving you many problems, the least of which is hot start problems. Your plugs are also suspect. I've heard some problems with those plugs in our bikes, but that's not always reliable info. If you want to do yourself some real good, get an MF AGM battery, and invest in a set of iridium NGK plugs. Your hot start problem should be gone.
You said you were buying an R/R. Why? Have you tested your charging system? Just curious.