OP: If it's not bucking by shutting down the injectors and it's acting more like a high speed ignition miss, then pulling and inspecting the plugs is in order, although this could still be be early fuel pump issues.
With both a bigger and higher flowing intercooler and the dp, you may have produced enough power and combustion chamber heat to have burned the plugs, cracking the insulation or to opening up the gap producing a high speed miss.
What plugs are you running, how are the gapped, and how many miles do you have on them? When did you last check them?
With both of the above mentioned mods, you are on the edge of needing one step colder plugs. If you went that route already, you may have fouled one or more of them from low speed driving.
It's cheap (free) to pull those plugs and look at them. If they are clean and there is no evidence of cracked insulation, etc. and they do not have a lot of miles on them, try regapping them, probably down to .028 or even .026 (certainly not more than .030). If they looked burned or overheated or the gap has opened up a lot, then you probably need one step colder. If they are fouled, then go back to stock heat range and gap the new ones properly.
If all looks good with the plugs, then one or more of the coil packs at the end of each plug lead could have started acting up.
Just a thought.