vagcom problem too many communication errors

I'm working on an 03 Jetta 1.8t converted to diesel, auto to manual. I'm using a manual engine harness under the hood. PO installed clutch pedal and did the wiring splice for the clutch override. Most of the relays were missing, went to salvage yard to see what was missing and where they go. I can read codes with vagcom but once I start the engine I get "too many communication errors to continue. Also the clutch override doesn't work I have to jump start it at the starter with key on. At a loss here, Help!