So I don't know if someone has had an issue like this before or not, but from what I can tell by the posts there isn't anything... I have a '95 GS500E, and recently the petcock went bad on me, causing gas to leak all over the place. I didn't have time to fix it myself so I took it into a mechanic and he replaced it, and also said that the carbs needed to be cleaned/rebuilt before it would start again.

He was going to charge me a crapload of money, so I figured I'd do it myself and see if I could fix the issue. After cleaning out the carbs and replacing a couple worn jets, I put the bike together. This is where I ran into a slight problem.

The bike started, but the engine idle was all over the place. I warmed up the engine, and then set the idle at around 1.5k rpm. But every time I accelerated, engine began to idle at close to 4k-8k rpm. (My tach is broke, so I'm estimating based on the sound.)

I figured I screwed up and didn't seat the accelerator cable correctly and it was getting stuck. But that doesn't seem like it was the case. Any ideas? (The bike is also at 50k miles on the engine.. I don't know.. could the engine be going bad?)

You have what's called high/hovering idle.  I had it too on my 2009.  It means your mixture is too lean.  Try reading this thread.  It explains it well:

http://gstwins.com/gsboard/index.php?topic=41199.0