Its almost certainly not the ECM. While its possible for an ECM to go bad, they typically fail catastrophically, not it runs rough and then runs great when warm. I still do tuning on these old GM OBD1 ECM/PCMs (been doing it since the late 90s) and aside from a bad write to a EPROM or FLASH chip, the computers almost never fail.
The CTS and the MAP can both cause rough running but not typically the way you are describing. Since you did an entire engine replacement, a damaged wiring harness somewhere is a likely culprit. Its odd that it runs rough cold and then no issues when warm, though, its usually the other way around as when the ECM is in open loop it is just using the open loop fueling tables. Once it goes into closed loop it starts using the O2 sensor and trying to compensate for any issues.
I know its not likely but if there is someone with a laptop, and OBD1 scanner, and a scan tool like Tunercats DATACAT program (its an updated version of the old TTS scan programs for GM OBD1) or a GM TECH1/2 you can use it look at the live data and see what is going on. Maybe its some timing issue that is causing it run poorly in open loop vs closed loop.
