I PM'd Glenn yesterday and suggested breakouts by stock, cafe, chops. Your suggestion would go under stock bikes.
It sounds to me like you're suggesting subforums for different bike types. Just like we currently have sections for SOHC/4 Bikes, Project Shop, Other Bikes, etc., you're suggesting sections for stock, cafe, and chops. Correct?
If so, I don't think that's the best option - issues faced by someone with a Cafe trying to get his bike to run correctly with the pods and 4-1 are going to be exactly the same as someone trying to get the chopper/bobber/slightly modified bike with the same mods. If anything, perhaps subforums for different areas would keep it a bit more organized - a section for engine mechanicals, one for electrical issues, one for tires/wheels, etc. This type of organization method is used on the Nighthawk forums I go to. The downside is that it's possible for a thread to go unnoticed if people spend all of their time in one subsection, and it's also a pain if an issue starts out in one category but turns out to belong in another. With everything getting dumped directly into the SOHC/4 subforum, stuff gets kicked off the first page pretty quickly, but everything typically gets seen.
I see the merit in doing something like the OP suggested - perhaps create a thread in the FAQ subforum for each model/year, then that thread can be used to post info and tips specific to that model year.