Ok, so here we go again..
I recently replaced my engine on my 91' GS to a 97' model Engine.
And the problem iv'e noticed (Happen twice or so in the last few days Not consistent though) Is when i start up the engine it sometime's pops (could be a misfire muffled) and it rides pretty rough and sluggish for a mile or so
(loses and gains power subsequently) fthe last time i just rode it at high rpm's for a minute or so and rode fine afterwards. I think i could hear some popping or something of that sort. then puffed a little smoke cloud - i think it was blueish or gray (couldn't really notice) behind me and went back to full power again running fine after that.
gas tank was full (Fresh gas) with inline fuel filter, new air filter + new oil.
rained a little at night before starting it but ran fine at the morning (rode about 24 miles to work cruised the whole way at around 8K-9K RPM) Problem happened on the way back from work after sitting for about 9 hours). Petcock set to ON (No PRI usage at all since engine replacement)
Carbs are probably STOCK so is everthing else.. (Not one hell of a mechanic and My budget IS pretty low..)
Any ideas anyone?
Could it be exhaust related? or is it more of a spark plug issue because they are supposed to be new, I have no idea where to start  from..
Any help would be really appreciated. (Can't sleep at night thinking i have a problem with my baby again...)
:dunno:

Oh and one of the times when the problem starting happened
I was with almost full choke on and i think i accidently pulled the throttle while trying to start (That's when it just popped and turned right off i think i smelled a slight gas smell after that but i'm not sure if it was related..)

oh, And i do have a little idleing problem (doesn't idle steady dies at traffic light stops... if i set the idle at around 1200, if set a little higher works better of course maybe i'll leave it like that...)

At this point the only thing I can think of is to rejet the carburetors.

If I try to start and fail (flat battery), then connect a booster and start, then I often get a backfire.  If I start on the first try, then I never get a backfire.  I think maybe the engine is getting some gas while I crank the starter, but there's not enough of a spark to start it.  When it finally does start, the extra gas vapor ignites... maybe somewhere in the exhaust?  I suppose it would make sense that if you're cranking it, it is drawing air in and pushing out unburnt gas vapor into the exhaust.

Just a guess.  But mine doesn't ride rough for the first mile (well not any rougher than it does when I start normally with a good battery charge), and mine doesn't kill at stop signs once it's had a couple minutes to warm, so maybe those problems you're having are unrelated to the backfire.