Stop guessing. If you think the alternator is bad, get a voltmeter and wire it in so you can glance at it in the cab while it throws a fit. Of course if the engine is not running well, the voltage will drop a little bit, so expect that.
No where in this thread did I see reading codes mentioned. I know these EECIV systems can be cantankerous sometimes and reading codes does not always lead to a solution, but sometimes they do help. I had a battle like you with random bucking and after reading the codes over several weeks a TPS code finally reared it's head, I replaced it, and all was mostly well. I still had a little buck in it once in awhile, especially when pulling the engine hard. That ended up being the pickup in the distributor, I got a code 18 in the memory codes.
Be warned if you want to change the module in the distributor, you have to pull the dist apart. But I would recommend doing that instead of getting a rebuilt dist. I bought the module and went to pull the gear off, and was not careful enough and broke some teeth. No one had a replacement gear. So I ended up buying a rebuilt dist from local parts store from Cardone. Installed it and it was worse than the one I took out. That gave me a clue I was on the right track. I took the Cardone dist back out, and was more careful this time and tore it down, they had not even taken it apart. It was full of old sticky carbon and black grease, the module was not even replaced. I cleaned it up, put my new module in that I had bought before, installed it and it ran great after that.