This is an auto file, you need to flash a manual file.
Also you read it as 1mb, but it's 512k.

Here's the correct file.

Sounds like all that was done was just the DTC's killed.

If that is the case you have to:
1. Flash the file.
2. Wire in the clutch pedal switch according to the wiring diagram for the manual car. Sounds like it's wired incorrectly. You can check that easily with VCDS, if it's reacting to pressing the clutch or not.
3. Disconnect the TCU that's dangling somewhere still (on LHD car it's in passenger footwell under the carpet), this will also remove the PRND321 from the dash.
4. At this point most likely the ABS is going to light up like a christmas tree. The auto one can't be recoded to manual, you need to buy a S6 manual or Passat W8 manual ABS, swap it and code it.
5. If the swapped gearbox does not have the same gear ratios as the regular S6 manual gearbox, you might need to adjust NVQUOT parameters in the file based on logs (or pay someone to do it), otherwise gears might be detected incorrectly and the cruise control will disengage at random or not work in 6th gear.

Good luck.