I haven't gotten to read this whole post, but I'm down with this concept so Ill post this before reading it all.
Honda vf700s. Bought it in April or around then for $700. It ran but not well. Went through a cycle of reading the manual (which seems to be for every 80's v4) and buying parts and putting the carbs together and trying it out and taking the carbs off and ordering parts and so on. Probably spent $1000 overall with a couple outstanding expenses that I know about.
Also, I almost burned this bike, like it was on fire and I was smacking it out with a shop rag. singed some of the wiring but not too bad.