The T-5 and T-45 are made by Borg Warner. Borg Warner bought out TTC, the Makers of the Tremec transmission. This has happened in the last 2 years.
The T-45 is rated at 330 ftlbs of torque.
The TR-3650 is rated at 365 ftlbs of torque. It is rated the same as the 3550, just made for easier shifting from the factory. The TR-3650 will mount to any 4.6 Mustang. The drain plug, shifter, and lack of speedo gear (TR-3650) are the main differences.
Back to the original question, I don't think you'll be able to get the speedometer to work. The 98 and earlier stangs were mechanical using a speedo gear, whereas the newer ones were digital. Don't quote me, but something to check into. If it were me, I'd trash the T-45 and get a T-56. It's not outrageously more.
TR 3650 sucks fatty too....i'm on my second one (synchros went out on the first one at 3800 miles)
If i keep this car for any length of time (read: if i don't get an '03), then i'll be putting the T-56 in.