My dad changed the ccm after losing interior lights, puddle lights and other comfort setting, after changing the ccm after finding it in a puddle he is starting to get the problems again such as electric seat adjustments not working, no map lights, he's left the ccm out of its original hole and kept it off the floor so it can't get wet but is still getting the problems. Any help appreciated

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Have you checked under the carpet under the passenger side at the back?

 

Check this thread....

 

http://www.briskoda.net/forums/topic/152490-water-ingress-problemsolved/

He said he's had the carpet up but can't find any wires, does the passenger seat need to come out?

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I think you'll really struggle to get access to the wires well enough to sort them without taking out the passenger seat.  Otherwise you'll no doubt end up with burnt hands and probably some melted carpet / foam from the soldering iron...!