car is cutting after starting

This may not sound fun, but start scanning. You're going to need VAGCOM software to finish that build. Did you also swap the ECU and TCU? It needs to be done if you want full functionality, and you need to make sure you get the key and ignition from the ECU vehicle. The car will run with the ECU programmed for an automatic, but you will notice when/where things aren't right. Lastly, you might just be in a security lockout if you did swap the ECU/TCU and did not swap the ignition. Program the keys if that is the case.