Did some research into the symptoms being exhibited - Fuel pump, injectors, ignition coils cycling on/off during starting event.
Used Coil and Injector test mode with plugs pulled - both worked perfectly. White/red 12v feed from ECU 1B rock solid, and grounds are good as well.
On to the CAS - as noticed before, timing was dropping off and intermittent. So, decided to manually spin the CAS wheel using my drill and observe behavior.
Same result. RPM drops off, timing seems awry, and Lost Sync Reason 38 which appears to relate to the 4G63 setting in MS.
Checked wiring at CAS harness:
Blk/Lt Grn: GND
Wht: 12V (Opto in -)
Yel-Blu: 5V (VR2 in +)
All the threads I could find stated that both hall sensors are fed 5v, that's incorrect. Correct voltages for 95 Miata is as indicated above.
Back-probed CAS with it plugged into harness, and spun by hand - observed 12V sensor fluctuating, but 5v sensor was steady. Pulled apart and cleaned CAS thoroughly, which made no difference. No visible wires to repair in CAS either, because hall sensor board is molded in plastic and non-serviceable.
At this point I'm 90% sure this is CAS related. Which is odd, because there were no indications of any issues prior to doing the transmission swap - and yes, the sensor was removed during the trans so as to not have the housing impact the firewall.
Will update tomorrow - getting a $50 used unit off Craigslist, hopefully.