Are all the frames the same from 1986-1997? For example will an engine out of a '97 (5 speed) bolt in an '88 frame? As far as any of you guys know did they change anything? Like, did the engine cases change when they went from a 4 to a 5 speed or anything else like engine mounting loacations. I want to swap my good '97 engine (with a tweaked frame) into an '88 frame (non tweaked) will it work?

absolutely nothing different in the frames from '88 to '02, that far I can say.
I would take the CDI with the engine, there might be some small diff with those throughout the years.
and I would prefer the controls out of the later too
if you take that might as well take everything.
mirrors are better with the '86.

Verslagen1 You are correct in fact they're still the same (09 S40 Blvd) According to my friendly local Suzi Dealer the Part # is the same from '88-'09. The only LS650 or Savage frame that were different part #'s are '86-'87. I picked up a wrecked "97 and needed a frame but was unsure of what years were interchangeable. The backbone and down tube are bent beyond any attempt for repair. I found an '88 from a Salvage dealer on Ebay for $99. Its on the way. I'll post pics of the project as it progresses.