OK... Here's the setup:

I bent my valves in the fall (too many teeth off after replacing the head gasket) I finally got around to rebuilding the head.  I put all new valves and seals in.  After putting the head back on (and tripple checking the timing chain and sprockets) my bike runs again (wouldn't even fire before).  It seems to drive strong... kinda... WHEN IT IDLES IT BACKFIRES THROUGH THE INTAKE EVERY SO OFTEN.... WHEN I OPEN IT UP ALL THE WAY ON THE ROAD IT SEEMS TO BREAK UP AND LOSE POWER.  IF I DONT OPEN IT UP ALL THE WAY (HALF THROTTLE) IT DRIVES JUST FINE. 

Here's my guess... I need your oppinion:

I checked the carb boots (as I was getting the notorious hanging rpm's) and one was cracked really bad... I'm guessing I'm backfiring due to that.  I've siliconed the crack until I can get new carb boots in.  The breaking up I think is a throttle issue where I need to adjust my throttle cable... (I hope)

What do you guys think could be the back firing/ breaking up in full throttle issues?

dose it just back fire  when you left off the gas ? i know if it dose that then its pretty possible you have a exaust leak .

no... it backfires when it sits at idle

When you say exhuast leak... do you mean exhaust valve leak or exhaust???  I noticed today that it does pop when I let off the throttle from time to time... It still breaks up really bad when I go full throttle.... GRRRRRRR.... still the popping out of the carb... any help???

Again... it pops at idle... and from time to time when I let off the gas.... more help???

Popping through the carb means one of two things, the intake valve is hanging down when the combustion starts. Or that the mixture is so lean that it will combust once the mixture meets a hot spot in the cylinder. Things to check are the carb boots(which you already have), the little vacuum caps that go on the carbs, make sure they are there and are not cracked or anything. Followed by checking that all the orings are in the carbs, becuase if you lose the little one at the top it can cause it to run lean.

ok... so could leaving my bike under a tarp in freezing weather mess up the carbs???

What exhaust are you running?

Well, I'm sure you know what you know (that make any sense?), but I thought my bike was backfireing through the carbs too. It seemed like a backfire, with a big bam, and it would shake the carbs a bit too. This was an idle issue I was trying to solve. It was mostly a problem because when riding, the power would leave. I guessed it was backfireing through the carbs during those times. It turned out to be a missing cap on one of the carb ballance ports. I only found this out because I ran it (was working on it, and someone was like, 'start your bike, I wanna hear') without a tank, and it poofed into my face air/stuff when I leaned over it. I stuck my finger on it, and wow (understatement at the time) it was fixed. Now, it could be that it still pushes backwards, but it doesn't cause any problems. I was thinking that it could be the timeing (like coll0412) but wouldn't that mean it constantly (every cycle) backfired?

*shortversion: could be an air leak. (er, reverse air leak?)

KYGS500E: I don't think cold would mess up the carbs, gas freezes at lower temps.. I don't know how much lower, but .. ya. Oh, and the carbs parts should be fine.. they arn't made of cheese. (cheese doesn't freeze well)

the coughing if regular like when trying to start its crank cough, crank cough,crank cough then its valve adjustment/timing.  if it starts and runs and while running its  like cough cough, idle idle idle cough, idle cough then its most likely a mixture issue be it improper jetting for intake and exhaust setups, or Vacume leaks around the carbs/intakeboots.  with these bikes its kinda rare but does happen something in the ignition system, Plugs,wires,coils,pickups,Igniterbox.     My GS is jetted ok, but when cold will cough or spit through the carbs untill warmed up.  check to make sure there are no Vacume leaks, i took my intake boots off, smeared alittle sealant on them and bolted them back on. from that point it was basicly Orings in the carbs.