Even Rocky runs stock TB at 1500hp , putting larger TB's on with ecutek it will drive like crap, intercooler will make a slight difference but at the boost a stage 4.25 can achieve stock ones dont work that hard on the street, on a track you may see some difference.
I made 1101whp on stock plenum, 1050 injectors, 2 pumps and stock tb's, the new GT35RS's being made we will still use stock TB unless I buy bthe TSM manifold but thats close to 10K so we will see.
At stage 4 the stock throttle bodies flow just fine. The downside with larger throttle bodies is that they are less sensitive, a 1% difference in opening will be a bigger difference in the amount of air they let through than the stock ones.
An example (just some math, nevermind units):
Say that you have a set of tbs that flows 1000, the stock ones flow 500. When you press the gas pedal to open 5 percent the stock ones will flow 25 more and the big ones 50 more. This means that they are impossible to fine tune as well as the stock ones.
Of course this is more apparent in city traffic than at the drag strip.