Hi Graham, sounds like an unfortunate experience there, but hopefully you can get it all back and working again.
 
	For the roof, you need to test with a multi meter that voltages are getting to the correct place, i.e. the correct fuse - remember that a fuse can "look" fine but only a resistance test would confirm, - the switch in the roof, etc. Can you hear any relay clicks as the roof switch is operated? In normal circumstances, the operation of the roof would not be linked to the replacement engine, but with Jaguar you never can tell.
 
	For the fan 1, could it be as simple as a connector loose / not reseated correctly after the engine installation. The fan should generate a fault code (DTC) of some description which can be read with an OBD code reader, which in turn would help point you in the right direction.
 
	N6 JMX