re: neighbor thought ant-theft would shut down fuel, I think that is correct also, the antitheft, when active, sends a signal/code to the ECM - but I'd have to re-check the ETM schematics to confirm this..
** re: relays - I'd be suspect if you had to swap (any) relays to get progress..
(If it was me), I would be considering replacing (both) relays with new, as a diagnostic step..
Crank/Cam sensor:
I would put the (original) crank sensor back in *the 5spd one,
and (swap) the cam sensor from the (original 5spd) motor over to the (new/donor) motor..
Did you have to disturb / remove the flywheels and crank position sensor ring from the motors during the swap?
That info may be important.
re: O2 sensor: -Providing the ECMs from both vehicles are from the same family-, then no, the o2 sensor should be fine: my '00 Sporty 5spd is running the exhaust manifold and o2 sensor from the '01 auto Sporty parts car here.
Fuel/Spark:
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If you have confirmed fuel, next would be pulling the top cover over the coil packs, hooking Intake plenum back up, and confirming you are getting spark w/ an in-line test light,
If fuel & spark are present, try shooting some starting fluid into the Intake plenum and see if it runs on starting fluid only,
If runs on starting fluid only, would pull the return line at the fuel rail (passenger side, follow fuel filter line down to it, return line is next fuel line), with a helper, jumper the diagnostic port to engage the fuel pump and note if any fuel is flowing through..
And would be using a probe light / NOID light to confirm injectors have positive voltage, and are triggering / firing..
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re: Old school, I hear you - the OBDII / ECM adds a level of complexity vs. a distributor and points setup...
I'd suggest obtaining an OBDII scanner that would allow you to view real-time data from the ECM.. my sig. has a link to the low cost (laptop/USB-based) one that I use here.