The Project Pad

I got this a few weeks ago. It is nice but I need to plan a 6-speed swap ASAP.

Auto trans is doing some weird things randomly.... couple of big clunks like it missed a shift then slams into next gear.... always seems to be in the wrong gear, like every auto trans ever.

Any pointers to a detailed 6 speed swap thread?

Find a c5 6spd car and get everything from it....

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^pretty much this. Manual trans was only an option on 2.7t cars in the c5 range and its a 4.11 final drive like the S4 so you will need the rear differential from the donor as well. I'm not positive, but I think this motor is similar to the 40v ART/AWN engine so a 2.8 30v flywheel and clutch should work. I think this generation ECU (ME6 ?) can be re-coded to manual with vagcom, but I would double-check that.