I think you can order a Transgo shiftkit online for $100... I was going to get one but I bought a stick instead.
I think the m6 is faster for a couple of reasons...
1) More Gears means less drop in RPMs after shifting.
2) M6 has 4 gears before overdrive, A4 only has 3... and extra power gear colud mean a lot.
3) M6 came stock w/ 3.23 or 3.42s, I'm pretty sure the auto came w/ 2.73s which will slow it's ass down.
4) Even if #3 isn't accounted for, i.e. both have 3.42s, I still think #1 and 2 are enough to make M6 faster, plus, in this case it will also have a higher top speed... just a bonus
If there are any engineers reading this and you know about gear ratios, please reply, the M6 has a better ratio than the A4 in every gear but 1st, so this should mean an A4 will only pull on a M6 in when they are in 1st. Just my thoughts.