That's sounds like your at your wits end, feel for you.
It was my understanding from reading about someone else's car with multitronic that the module you mention is attached to the gearbox and not inside the car, if thats is true then the gearbox fault should be unfortunate but not related.
Unless the scuttle drains are leaking down over the gearbox ecu, but like I said I don't know about the multitronics so don't know where the ecu is on the gearbox or where it is in relation to sources of water.
I remember reading on a forum somewhere that the multitronic ecu has a weak point on a connector inside the case that goes intermittent like a dry solder joint, and can be repaired reasonably easy if you have the tools and soldering skills, I think that's what the chaps on eBay are offering when the repair your ecu.
If I can find the forum I will post a link
Might be worthwhile checking the harness to the gearbox too before you go further and spend lots of money.
I hope you get it sorted out.
Found this site, it shows what I was talking about, on the a4 multitronic ecu picture with the broken wire.
http://multitronic-box.com/tag/gearbox-ecu