Your heat problem I would have frist checked out changing the Thermastat (I'm betting it has not been changed in a LONG time and is hanging closed). At this point of running it for long amounts of time and miles where the car attempts to run hotter then it should, may have caused additional damage.
Unfortunately, I am not able to draw my own conclusions on your description. But I have some ideas (and if anything, they are just good maintanance).
- Change the plugs and wires. Those are cheap and can be a common cause of problems with rough idle or lack of power at higher RPMS. When doing so, keep track of the plugs and which cylinder they came out of. If you have some that look really bad, it can be a tell-tale sign of other symptoms.
- Start inspecting the coil packs if the plug/wire change does not resolve the issue (condition of the plugs might help determine a faulty pack since each pack is responsible for two cylinders, if two plugs running off the same pack look messed up, I think you found your culprit). My '94 Grand Am had an intermitant coil pack that randomly caused the car to run like crap (and originally it was while on the freeway). I went through about a month of insanity to find it was a coil (on accident). Using an OTC scanner I found when it ran crappy, the Injector Pulse Width was REALLY high (car was running more fuel to compensate for a misfire). I found the coil on accident when I was wiggling wiring harnesses (if I put my hand on the coil a certian way, I found I could make the symptoms appear/disappear at will). I knew the coils were all tight, I had a spare swapped it and has ran fine for over a year. I since found this write up about the coils:
http://www.pontiacbonnevilleclub.com...hp?f=48&t=1683
- An item I think least likely, but takes little time and a free check is the iginition module. It sits under the 3 coil packs. Just remove the coils (two bolts each, remember there order, leave the plug wires attached), remove the 2-3 wiring harnesses on the module. AutoZone (at least my local one) can test these. It's FREE. A friend of mine had some nasty performance problems and turned out, his iginition module was bad.

I hope some of this is of help for your situation.