Use Rdx injectors with a FPR if you can. OK they're "a bit" overkill but I noticed my car was runing smoothier and gained a few hp/tq almost everywhere (ectune remap). My AFR values are much more constant than with OEM B16a2 injectors.
Concerning the skunk2 IM which one are you talking about ? Because one of them is very similar to your OEM manifold.
You should get an OEM manifold ported and polished with a spoon style throttlebody and an ELR airbox. FC design belgium makes the ELR airbox (around 500€) but you need a huge amount of space to install it, move your radiator and modify the front frame of your car. it's expensive and a real pain to fit it but definitly it breathes a lot and worth it. I remapped a friend's EG6 this week, the old intake setup was ITR airbox + K&N + ARC intake chamber and we went from 13 AFR before to 13.8-14 AFR from 6k RPM to the rev limiter.