Without opening the engine to raise compression stage 2 cams will not perform well on a b16b.
I would not recommend a 70mm TB or S2 intake(assuming pro series which is almost identical to the type r intake). A Toda style 4-2-1 exhaust manifold coupled to a 2.5" decat and catback and then a...
If that is the picture of your current wiring harness from the D16Y8 it would seem your car is OBD2A wiring, in which case the PCT Ecu should plug straight in.
The best option is always a custom tuned Ecu. I believe I done a back to back test of Spoon Ecu vs Custom tuned obd1 Ecu some time ago, can't remember if I posted in on here or not - will try locate it.
I've setup 24XX cams on a b18c with Wiseco 12.5:1 pistons and there was no issues with clearance. Providing the cams are degreed correctly and Ecu tuned correctly it will idle nice and smooth.