Have you tried Re-Sync'ing?

Seriously, It could be heat induced, but then the problem should get better when it cools. Heat could affect wiring, vacuum or minor mechanical bits.

Your problem sounds very much like fuel delivery or spark.
Do you smell excess hydrocarbons from your tailpipe? This would mean incomplete ignition and electrical problems. Check the spark plugs. If it's wiring, I'd just take it in and have it fixed.

You'd hate to take it in for fouled spark plugs or clogged fuel filter though.

Good luck.