2001 Ford ZX2 seems like it doesn't want to change gears sometimes?

It seems like maybe a few times per week or so, it starts straining as if it can't switch into the next gear. Eventually it switches over and goes days or a week or so without doing it again. Then it comes back, goes away, etc.

The whole transmission was rebuilt just about 2-3 years ago.

So i would suggest the overhaul on the gearbox was not as good as it should have been. As a result you now have further issues.

Definitely a problem in the rebuilt gearbox. How many miles have you gone since the fluid and filter were changed in the transmission?