B16a2 swap throwing code 3, I've tried a couple things
 

Alright so I swapped in this b16, fully rebuilt to OE specs. Timing is set, valves adjusted, fluids added, ECU is a p28 with phearable basemap, ecu is known to be good and working. I pressurized the crankcase and started it up for the first time. Started no problem. Throwing code 3 however. It runs a little rough.

Code 3 is map sensor, so I replaced it with a known good one. Reset the ecu and tried again. Code 3 again. Checked my vacuum lines, seemed good, so I replaced the line just in case and used a T to tap into the vacuum for the FPR. Same code. There's no vacuum leak, putting my hand over the throttle shuts the motor off.

I had to extend my map sensor wiring, I am most certain I put it back in the right order.

Short of testing my whole harness, what else could this be, other than a wiring fault?

Its gotta be wiring or pinning at the ecu, no?
Id double check where you did the extension as well!