Intermittent loss of power

After a summer of working on the truck, it is finally up and running well for the most part, but I am experiencing a strange loss of power occasionally in 2nd or 3rd gear around 2000-2500 rpm. I press the accelerator and it almost feels like it isn’t registering, but if I let off for a sec and accelerate again it’s fine.

I’m trying to narrow down what the problem may be and want to know if I am doing any damage continuing to drive it.

Additional info:
2000 2.7l 3rz Fe 5 speed 4wd

The truck had been sitting for a few years until we put a new motor in a few months ago as well as a bunch of other new parts.

New fuel injectors
New spark plugs and wires
New fuel pump (bought a cheap one and is kind of my suspicion)
Cleaned MAF sensor, looks okay
New O2 sensors
New fuel and air filters

Could it be a clogged cat or bad crank position sensor?
Calibration issue?

Appreciate any thoughts anyone may have.

 

If these have a throttle position sensor, I'd check that out.

 

I may have completely overlooked that, it would make a lot of sense.
I think I can get one in town today, I’ll give it a try. Seems like a fairly cheap fix if that’s the case.