I've never heard of the auto trannies having any issues with the new downpipe clearing the transmission, but I know the manuals had some clearance issues (mine did) with one of the "holding fixture ears" on the case. Almost definitely you will need to flatten the pinch weld on the firewall. I also had to slightly dimple the new downpipe to keep it from hitting the passenger side up-pipe. See Step 26 and the illustration in the attached. Cheers!
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