Too much heat?
 

My car has a WAI, full grill block, and slightly larger gapped plugs (Actual .45 VS Spec= .40-.44)

On longer trips after driving for at least 45 minutes or so it seems to have a slight hesitation or break up while accelerating in lower RPM (2k-2.5k). Anywhere after that it seems to run OK.

I did a tune up about 4k miles ago but I'm wondering if this is too much heat that my engine is ingesting? Any ideas?

It's tough to say how much heat is too much, but clearly you've added heat and now the car has some hesitation. Try eliminating one of the modifications and see if it helps. If not, return to it's modified state and un-mod another part. Maybe try removing the WAI, then reduce the plug gap, or add a small hole in the grill block to see if any of those was the cause.