Touran bke to bkc conversion problem

[Chris pen]

Hi guys. 2mths ago my bke engine siezed after the turbo blew and emptied the sump in less than 300 yards. I have installed a bkc engine out of a 55 plate A3. "my car is an 08 plate touran. The garage are having problems as the car is stuck in limp mode. Its showing a crank senor error. Due to this the car is hard to start and when started will not go over 3000rpm. Is it because this older type engine uses a crank sensor the tourans computer is not compatable with or cannot understand the reading the crank sensor is sending back to it? Really stuck in a rock and a hard place here as they dont know what to do next. The car had a stage 1" tune months before the turbo failure to, could the tune be corrupted due to the battery being disconnected so long for them to do the engine swap over? Any advise would be great as this car owes me 5k now with buying it and now the engine change. Be a shame to scrap her if we can fix the fault. Thanks. Chris. 

[Volkswagen Owners Club]

I wonder if the flywheel/flexplate or crank sensor toothed wheel may have the incorrect number of teeth which can happen with engine changes 

Alternatively, maybe worth having the standard Map loaded onto the ECU to eliminate that as a potential source of the issue?