Have you considered changing the fluid and filter again? If your filter was clogged, perhaps the new fluid flushed more particles out of the system?

What kind of fluid did you fill it with?

Do you think that once the transmission has a certain number of miles on it with no fluid changes, it's best to leave it alone?

Sorry for all the questions, there seems to be some debate on this issue and I'm just trying to gather as much experience as I can ;)

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2001 S8 - Racing Green Pearl Effect