Screw a TKO, I had one, never again. Thing shifted like a dump truck and locked me out of 2nd more times than I can count.
If you are going to stick with a 5 speed just get a built 3650 from Stan at Pro Force Performance in Atlanta. He has a website with all the different options. Mild to wild. A 3650 with all the fixes done is butter smooth and can take a LOT of power. I know, I had one and swapped it into my 98. Need a Stiffler's crossmember, a good Energy Suspension 94/95 style trans mount and a Speedcal to convert the 3650 OSS speedo signal to 98-down VSS. I did a whole writeup on how to do it on here I can find and link to if you wind up going that route. Get one with the .62 overdrive to drop your highway RPM down a little.
Swapping to a 6R80 automatic is another option. Tall ass first gear it has would be brilliant with a B headed Cobra and the right rear gears and its a direct bolt in with a trans controller.
Manual if not a 3650 then Magnum. Its $$$, its worth it. 4.30s out back and the wide ratio one you will still have a super nice RPM on the highway with that .50 final OD.
I currently have a 99-01 style T45 myself and it shifts spectacularly with a Tri-Ax. I run basic Castrol Mercon V in it, 3.2 quarts and am gonna run with it till it breaks. Car is easy to shift at 7K+, actually the harder I thrash it the easier it shifts. 2nd is notchy sometimes when its cold or I'm at a low RPM and I often have to do "1st, 1st, reverse" which I never had to do with my 3650 but that's minor stuff. Trans just turned 38k miles old lol. If it does eventually crap out since I'm in Europe now my options are to teach myself how to rebuild a trans or figure out how to get a Magnum out here without losing a limb in shipping/taxes.
-2000 Mustang GT Steeda #0048. 4V swapped, FTBR IRS, Steeda factory suspension, Ultralites, VRS X, "Exhaust Shop Special" catback.
Stock 2V computer rewired for 4V, Tuned by James Gordon.