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LMAO!! The word FLUSH and TRANSMISSION normaly go with an automatic transmission. That is why we jumped on making sure that you had the A4 Procedure in mind.
New ATF in the trans will make it shift a LOT better.
AMSOIL has a FANTASTIC ATF for the C5 A4! That would be my recommendation. You will be able to drain out and refill 3.75 qts. It is compatable with ALL C5 manual transmissions.