Auto foxes have a Tranny-Line pressure adjustment in the throttle linkage called your TV cable adjutment. It might be out of whack too with the new setup.
I had an AOD 90 once and always ran it down to a local shop to have them check it after I was done tinkering (until I thrashed it for the last time and went with a manual C4 that kicked a$$)
http://forums.stangnet.com/showthread.php?t=624568
Bump the idle up too.. around 800 in neutral/park would be a good start
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2003 10th Anniversary Cobra Convertible
All Stock and staying that way... well maybe some pipes since it's so quiet..ahhhh! it's a sickness
1995 mustang GT vert - all black (almost back together)