Good practice to renew Your temperature sensor located on the side of the block underneath the intake pipe and your small fan might of had it mine did and it sounded like a jumbo jet taking off after shutting down the engine
Indeed. That sensor is notorious and has been revised numerous times since it was first introduced in the 1.8T/R32. I did mine alongside a new stat, both parts from VW. The sensor isn't cheap, mind. £45 I think I paid for it.
Had zero issues with the fans afterwards, so this is a curious problem!
I've heard if the fuse for the smaller fan blows, the second one takes over, so you could be onto something there.
As the fan controller is built into the fans, troubleshooting them isn't easy, but it's all tied into the after-run circuit that also runs the electric water pump for 5 mins after shut down. Dan, did you disturb the electric pump connection?