Where to begin... I have a 2008 Mini Clubman base model that had a sunroof leak. Water pooled in the passenger footwell and played havoc with the computer. Car would crank and not start - dealer said computer was corroded and needed replacement. After much $ and new computer, car running like a top again. I was assured that water through sunroof was because sunroof had been left partially open. San Diego had it's first heavy (for San Diego) this last month and water pooled in passenger footwell again. Checked it myself and found sunroof drain clogged. Car was wonky with weird electrical messages and back doors would pop open randomly, so I dried it out and let it sit in the California sun to dry thoroughly.
Went to start today and battery was dead. Jumped, and engine would crank but not start. I seem to have come full-circle and would hate to think a new computer is again in my future. Any suggestions?

 

How did you dry it out? Did you remove the computer and dry it?

 

First bailed it out, Then wet/dry shop vac. Then fan with doors open. I'm not actually sure where the computer is... perhaps near the interior fuses?

 

The Body Control Module is behind the kick panel just in front of the passenger door. It is the thing that gets wet when the sunroof drain gets plugged or comes loose.

You could try removing it and clean it with 99% isopropyl alcohol or electrical contact cleaner. Either will dry it out and not leave any residue.

 

This needs to be moved to the 2nd gen Clubman section, but if you got water in the floorboards you need to inspect the JBE (passenger kick panel) and the FRM (drivers kick panel. Depending on which drain fell off you probably have water in one or the either or possibly both if both drains came off.

I've fixed multiple cars that the JBE and/or FRM have been drowned, the level of difficulty goes from getting lucky and just drying it out and replacing the module, to having to cut and repair the wiring for every connector on top of replacing the module. The worst one I have seen I ended up rewiring something like 168 pins on the JBE and installed a new module, that was a painful day..

 

Going to move you to the Gen2 area. Us Gen1 folks don't know too much about them Gen2 autos with all those fancy doodads.