What size are the bolts that hold the cv axle shaft to the transmission. I know it requires a 12 pointed bit but what size?

Depending on which year A6, engine and transmission, it may be a 10mm tripple square.

Its a 2000 A6 2.8L Quattro with an automatic transmission

on C4s are 10 M (XZN of course).

not real sure.. looks like 8 and 10mm. Seems there also tree different axle used too...

TORQUE SPECIFICATIONS
Application....................................... ....Ft. Lbs. (N.m)
Axle Shaft-To-Transmission Flange Bolt
M8 X 48...............................................3 0 (40)
M10 X 48..............................................51 (70)

Axle Shaft-To-Wheel Hub Hex Bolt (1)
M14
Step 1................................................. 85 (115)
Step 2................................................. Turn An Additional 180 Degrees
M16
Step 1................................................. 140 (190)
Step 2................................................. Turn An Additional 180 Degrees

Boot Clamp (Stainless Steel)(4)................15 (20)

Heat Shield Bolt.....................................18 (25)

Upper Control Arm Nut.............................30 (40)

Wheel Lug Bolt
Step 1 (2).............................................37 (50)
Step 2 (3).............................................88 (120)

(1)Manufacturer recommends replacing with NEW fastener after disassembly.
(2)Using a four-way socket wrench, tighten crosswise.
(3)Lower vehicle onto ground, and tighten bolts crosswise.
(4)Torque for stainless steel boot clamp is for use with Constant Velocity Joint Boot Clamp Tool (VAG 1682).