OK i have a 2005 a4 avant with 125000 miles on it. Had what i think was a mis fire, wife was driving it. took it to the transmission shop they pulled the pan and found metal in it. first, replace or rebuild the tranny, or how much life do u think is left in it? Second, engine, some codes came up dont know what they were but should i just have the engine seviced and see what happens?

 

They pulled the pan & found metal in it!!!!!!! That is the oldest trick in the transmission shop book! The fact that they do not have the cabability to check for codes in the tcm tells me they should not touch your car to begin with.
Bring your car to a European car specialty repair shop , have them check the codes first before pulling it apart!

If your car does need a transmission , have a them install a reman from a certified ZF rebuilder like Ericksson Industries. That way it will most likely be done correctly & have the latest updates installed.