sounds like you may need a new map sensor. maybe got messed up when it was hooked up wrong. you should test it to see if its working properly. if that is giving buggy readings it will affect the injection causing it to lean out and richen up and all that stuff enough to do what your saying.
http://img.photobucket.com/albums/v6.../mapsensor.jpg

If the voltage is fine on that then I would check your timing. you said the bike was looped, it is possible that teh shock could have let the cahin jump a tooth. esp if your cct is weak as the f4is are known to be. I would check those voltages first and then check the timing marks make sure they are still right

 

Hmmm i guess ill have to look into that. However i figured if the map sensor did get screwed up that it would be throwing a "FI" like it did when it was hooked up incorrectly. And as far as the timing goes that is a possibility however there is a manual tensioner on it. Actually scratch that i flipped it when it still had the hydraulic so i guesss it is a possiblitity of being a jumped tooth. I havent looked in the manual but is it difficult to check timing on the f4i? Thanks again for the replies everyone they really help.

 

Not sure. would more or less require finding top dead center and removing the timing cap off the side. I can find out for sure in the repair manual if you would like. and Even though there is no light coming on doesnt mean there isnt a problem with it. it may be within range, but reading off enough to cause your erratic problem. Also did you run the bike with the manual tensioner at all before this started happening? maybe it the timing moved when you installed that. Just a thought since you said it had the hydro on when flipped and I assume when you repaired the bike you swaped in the manual. The way it sounds is like it may be a slight timing issue, I am not sure how much one tooth would throw it off, but maybe even over or under tensioned could cause the timing to be off just enough to act up a little bit.. I have never had this particular motor apart myself so its hard to say. I would def put a meter on that sensor first and try that.

I mean you pretty much have it narrowed down to 2 things that can very well cause these symptoms.. I would venture to say if the timing was off by a whole tooth that you would really know it through all the revs though. but if there is some slack in that chain it may be advanced just enough to cause that, same if it was over tightened could be retarded just enough to have some issues

 

hmm...yes you are correct that i installed the manual while i had the bike apart. I thought i did it right but maybe not. I loosened it till it started to slap and then tightened it up till it was gone. Ill try to get the multimeter out there today after work. I really feel as well if it was off by a whole tooth it would be noticeable in all the rpms. Maybe the chain is too tight or something. I noticed sitting a light this morning that if you hold it just barely past no throttle it will sit at 1500 and vary b/w 1500-2000rpms almost like it has a cam in it or something. THanks again for the help so far hopefully i'll figure this **** out today at somepoint.