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Has anyone out there had issue with a 2003 Acura TL with a replacement transmission ??  

this is for a 02 but maybe the same thing this is from the newsletter acura sends to its dealers service dept. check out acurazine.com and search the forums they might be able to tell you if there were recalls or any major problems

Axle Seals Leak ATF,
Roaring Noise, Erratic Shifts
If you are working on a ’99–02 3.2TL or ’01–02
3.2CL that has an ATF leak, erratic shifting, and/or
transmission noise, it could be caused by a worn
or damaged differential carrier bearing. If a
differential carrier bearing is damaged, the
transmission must be replaced.
• ATF leak - If the differential carrier moves
around (because of damaged bearings), the
axles can exceed the sealing range of the axle
seals and leak ATF.
• Transmission noise - Worn bearings allow
the differential carrier to move, causing
irregular countershaft gear to ring gear angle
and differential carrier bearing contact. This
often causes noise that has been described ***
a roaring or moaning sound.
• Erratic shifting - Contamination from the
damaged differential carrier bearings can
contaminate the fluid and foul the shift and
lock-up valves. A DTC that typically
accompanies damaged differential bearings is
P1750 (mechanical problem with the hydraulic
system)  

http://www.automotive.com/2003/49/acura/tl/recalls/26905.html

might help, although i doubt your car has less then 15,000 miles