GRANGERHEATCOOL

My 1999 A4 engine self distructed after a long heard unknown noise turned out to be a broken timing chain belt tensioner that let go at highway speeds. Due to the fact the engine had 170,000+miles, not much money, and being given a 2001 A4 engine with only 95,000 miles, my brother who is a full time well seasoned mechanic, decided to swap engines. The 2001 had a blown turbo which he swaped with the 1999 engines fairly new turbo.After several other necesary modifications such as:using the 1999 valve cover due to ignition coils location, modifing engine mounts, and cooling hose, grinding down end of flywheel a little due to the fact 1999 is automatic and 2001 was a standard transmission, the engine was ready to start.
Now, the engine starts for a second, and shuts down with no fault codes generated. It is getting gas, and power, but will not keep running.
I would really appreciate any ideas on what the problem may be. Thank You in advance for any help. grangerheatcool