2007 GS 500f...inconsistent throttle

[Rorshach]

Helllooo....

So I don't post here often, but I've found this forum extremely helpful in the past.  I've been having this problem with my 2007 gs 500f (12000 miles) for the past couple months:

Basically, when I'm on the highway, after about 15-20 miles of riding, the throttle just gives out, the bike changes it's pitch really low, and I can't accelerate past 55mph. At first, it was just kind of burping, but then it started lasting longer (and I even had blue flames coming out the exhaust).

That was a couple months ago...so I took it in for a full service, and they told me that the fuel/ oxygen mixture was off, and a vacuum tube was broken.  So they fixed it and it ran well for another month.

Now it's started doing it again, I put some gas mixture-carb cleaning liquid in the tank  (twice) and ran it for a couple weeks.  This helped a lot! And i almost thought that fixed my problem...I immediately felt the bike's power come back, and it didn't lose throttle for another week or two.  But lo and behold, I just got back from work and on the way, it was almost as bad as a couple months ago (where it was lasting longer instead of burping).  I'm taking the bike in this week for some other work, and I really don't wanna spend 100 bucks on a full diagnostic.  A lot of people at the shop asked me if it does it in cold or warm weather...Honestly, it doesn't matter but historically I've noticed my bike runs terribly in cold weather.

Does anyone have a clue what's going on with my bike and how I can get it fixed??

Other useful info that may matter: 
-I live in AZ. 
-I ride 30 miles to work 1-2 times a week since Oct 2010 (since then my bikes been having problems). 
-I have an alarm hooked to my battery, and every winter, my battery dies out overnight and I have to constantly use the battery tender to get it started


Thanks for reading my problem! (sorry it's long-ish).  I'd really appreciate genuine feedback on this issue.  It's my only way around!!! 

[Big Rich]

Well, a new battery could work wonders but I don't want to say that's the problem. Do you have the stock intake (with clean filter) and the stock exhaust? Also, are you running with the petcock in the prime position? Just curious.

If the petcock is starving the carbs, it will cause a high rpm lean condition- which causes power loss. And cold air is denser than warm air (also causing a lean condition). That's why they asked about that. If the carb cleaner helped a lot, it could just mean your carbs need cleaned. It's a lot easier than you think, but devote an entire day to it (removing, cleaning, and re-installing).

[Rorshach]

The bike does have stock intake and exhaust...as for the filters, when I got the service done, they checked all the filters and replaced the ones that needed it.

The petcock is never on prime.  Only On or reserve if I just ran out of gas.

[noiseguy]

Try running it on "prime" and see if the problem goes away. If so, the vacuum-operated petcock is the issue.

[Rorshach]

Running it on prime didn't help...it ran just as bad, if not worse.  Also, it's starting to do it a lot sooner, as in I don't have to ride at 70 mph for 10 miles.  It did it during a 3 mile ride at like 40 mph :/

[BaltimoreGS]

Could it be one of your cylinders is cutting out on you?

-Jessie

[Big Rich]

Guessing there's no inline fuel filter? Maybe the tank vent is clogged. Try opening the gas cap a little and see if that helps.