Definately do the TPS, but I agree with Ryan here, sounds like your cam timing is a little out - maybe inlet cam 1 tooth advanced or something similar (advancing the inlet cam is what VVT does afaik).
Timing is an easy one to get slightly out on the 4AGE (apparently) 'cos even Toyota has done it wrong on a couple of engines I've seen.
Planing 0.5mm off the head should affect things too much, in old skool talk it's only about 20 thou or 0.020 of an inch. This sort of increment is normally used just to true up a head, with the (marginal) rise in compression as a by product.
The amount it will raise the compression depends on where the majority of the combustion chamber is located...(head or piston top) The other thing to think of is that afaik the 4AGE is a non-interferance engine, and what you're effectively doing is bringing the valves closer to the pistons.... Once again tho, 0.5mm isn't much I guess.
My 2c.