This is my very first post. You guys have already helped me a lot and I hope to become knowledgeable enough to help someone here too. Here's my problem- I broke down and paid a shop to rebuild my carbs in a rush to get on the bike for the first time before this past winter. I didn't have the bike running until after they did that and replaced my CDI box, so I have nothing to compare it to. I ride it for maybe 30 minutes or more depending on how hard I'm pushing it and then it dies. It starts back up after 2-5 minutes of waiting on the side of the rode. I also top out at maybe 60-65 mph, which again I don't know if that's normal or not. I've had friends suggest its flooding itself or its letting in too much air and over heating. Either or it would be the shops fault in tuning the carbs wrong correct? Any help or suggestions would be greatly appreciated.

my 97 did this. sometimes it would be sooner then 30 mins of riding at highway speeds. try riding with the petcock on prime. this resolved my problem along with cleaning out the fuel tank cap vent. if your vent needs cleaning you can check it by riding it till it dies like you said and then open the fuel filler cap and listen for a woosh of air.

You should not have to set the petcock to prime.  Are there any inline fuel filters? If so get rid of them.

It's more likely a fuel delivery problem than a overheating issue.  Possibly even incorrect jetting.  When my 2009 was stock I had it up to an indicated 95MPH; now with upgrades it gets there faster.

Mine did exactly what the OP stated...sooooo embarrasing on my first night out on it on a group ride....still having trouble fixing it

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Most likely starving for fuel, with a stock GS you should have no problem riding at 90+ MPH all day, Check your float hight using the tube method 

Mine did the same, it was because of fuel starvation. I've experienced it one time that some rust in the tank clogged the gas filter, and another time when I installed another filter between the petcock and the carbs: it was too big, there was always some air in it and the lowered pressure starved the carbs of fuel  .

It could also be a faulty fuel petcock, try running it on PRI and see if the problem is still there. If it is, I'd check the fuel filter for any clogs and then the carbs. In my bike I made a small mod on the petcock (it's in the wiki), so it wouldn't need vacuum from the carbs to operate, like a constant PRI. I haven't had any problems since, in fact my bike now runs a little rich. I'll have to adjust the air screws as soon as she gets back from the shop!