Swapping a NB2 head & engine harness into a NB1, run NB2 Megasquirt?
 

Edit: Ignore monologue, I've independently come to the conclusion that keeping wiring/ECU '99-'00 is simpler since I'm looking for VICS & VVT support.

TL;DR: previous owners stuffed a low miles '94 long block into a '99 NB1, and made an unholy engine harness splice of a combined '94 and '99 harness. I am both terrified and impressed that they got it running. We have a spare VVT head. Based on what I've researched, I can source an NB2 engine harness, deck and swap on my NB2 head, and run it with a NB2 Megasquirt without issue?

Back story is that I picked up this '99 NB1 Miata for $950 Sunday, just got the title. New-ish top, but it isn't lined up correctly to get a good seal. We technically did get it running, but the unholy '94/'99 fusion harness is going to be a constant source of problems. Best to start from scratch with a new engine harness. No real rust, all 4 cylinders show ~150+ PSI even compression on what I learned is a '94 block, NA8 '94(?) intake, and what I assume is a '94(?) head. Body has 118k and is in good shape, engine unknown but has pretty good compression for a nearly 30 year old motor. I already have a spare '01+ cylinder head pulled from my K24 swap donor. I'd like to swap on the VVT head onto this '94 block and wire it with a non-fucked-with 2001-2005 engine harness. 2001-2005 Megasquirt3 should allow VVT control through the NB2 harness, and based on what I understand, it should just be plug and play after swapping the harness out?

Or is the solution to just run a replacement '99-'00 NB1 engine harness and run a MS3 that has VVT add-on support? Get non-mangled NB1 correct harness and just run new wiring for the VVT?

I've been doing a research binge, I'm not sure I fully understand the wiring consequences of either.

Edit: after 15 hours between wiring diagrams, being at the OMV, working on the car, and reading on the forums and tech documents...I've come to the conclusion that it probably best to source year-correct ('99-'00) engine harness, year-correct ('99-'00) MS3 that supports cam phasing & VICS, and run a new wire for VVT control. If anyone thinks this is incorrect, please let me know.

Yes, you always run the MS3 specific to your shell/wiring harness. You don't swap the harness. Adding vvt is trivial.