Currently own a 2007 Focus MK2, would not start and found it was the alternator that needed change. After getting a new alternator everything seemed fine, until I realised the rear wipers, front wiper washers and radio would not turn on, the front windshield heater light is also always on and I cannot turn it off, also the electric windows have stopped. I have checked all fuses and relays thoroughly and they are all fine. If anyone has the same issue or knows the issue I would really appreciate it. 

Also forgot to mention, windows also not working. 

All functions that are not working (correctly) are controlled by the GEM module. On the Focus MK2/MK2.5 the GEM module is fully integrated into the interior fuse box (it is basically a fully computer controlled fuse box).

You should start checking all electrical connectors of the GEM module/fuse box. On the Focus MK2/MK2.5 it is a known problem that the connectors can be kicked loose by a passenger. If all connectors are still connected and locked the GEM module/fuse box must be considered defective. 

Cheers for that mate, I have completed a GEM test by holding the rear window heater and waiting for the beeps, everything seems to be getting a signal.