This is getting rarer and seems to be working its way out of the car...

Sometimes once the car's fairly warmed up and been running a while, the idle will want to stick at about 1500 or so, and acceleration will be mediocre and a bit intermittent... On my first trip in the car the power would occasionally just cut out, but it doesn't seem to do that any more, just this idle/choking up problem every once in a while, 50% of the time the car is fine.

I'm chalking this up to the car having sat for the last two years... And driving seems to be making it better so I don't plan on worrying about it. what component specifically might be related to this though?

Could be your BCDD or if it's a California car, and I seem to recall you saying that it was, it could be you altitude switch. What to do about it is covered in the FSM.