to the OP,
since you don't appear to need the education on how to read, comprehend, understand, and properly respond to a post, you can skip all of that.

given the way you describe what is happen, here's my 2 cents,
check the MAF sensor plug.
if you're aftermarket intake isn't secured, it is more than likely bouncing around causing stress on the MAF sensor plug, wearing it out, making it loose.
All it would take is the right bump for it to briefly loose the connection and that would cause the ECU to think the MAF just failed and start to go into limp mode, retarding the timing, dropping rpms, and dumping fuel. Which, especially in an automatic, would feel like a loss of power. And since it only lasts a moment, it would feel like a split second loss of power.

Nothing else really fits, unless there are other symptoms we don't know about.

any why do you think it takes a long time to get passed 2nd gear? you mean you are in second gear for along time? or the shift from 2nd to 3rd takes forever?
If it is crappy shifting, then the fluid is probably old as hell.
as for being in 2nd gear for a long time, I guess that depends on what you are comparing it to. But again, could also be fluid issues.
I would drop the pan, let it sit for a few hours at least, get a fresh filter on there, top it off with fresh fluid, and probably even toss in a bottle of lucas transmission fix. Especially if it has a bunch of miles on it. people tend to forget that the auto tranny needs maintained like everything else on a car.