1.8t Dashboard Loom

Hi, I'm putting a 1.8t into a shell as a project. The shell is drive by cable, was automatic and had the 1.6 8v AEH. The 1.8t is coming from a 1998 manual donor Golf with the AGU code which is also drive by cable. My question is, would I be able to use the dashboard harness from the Golf in the Octavia without issues? 

My reason for asking is because the AGU loom is a manual loom, and the shell is automatic. So besides the obvious differences in engine I will also need to deal with wiring to make the car know it's manual. Can I swap the dash looms, or would it be best to alter the existing dash loom under the raintray to make the engine work?