I've been through this with a couple MKIIIs and I know a few others who've been there too. It's a royal pain and typically is due to more than one point of failure or something which the ECU and the TSRM don't know how to diagnose (such as a short in the wire harness across two lines such as Vc and Ks.... been there, rebuilt the whole harness). With diligence you'll find it it just takes patience and a lot of deep breaths.
Now that you have an ECU that you're more confident in in place you should check for error codes regularly to see if it sees something we haven't.
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