Not exactly an apples to apples comparison, but some info for you based on my experience.
I installed a t5 trans, with a .63 5th gear, into my 64 390 (t-10 4spd.) car earlier this year.
I agree with your choice for the tko, especially if your engine is going to be higher hp and you plan to race it or drive it hard. I just cruise mine, so the weaker t5 should be fine for a while.
I had the same questions as you. Bellhousing choices, and input length etc. I ended up using an adapter plate on my stock bellhousing, from here. https://transmissionadapters.com/
I spoke with them on the phone and emailed them pictures and depth and bolt pattern measurements of my stock bell, because they have several options, and the owner insisted on making sure he got me the right plate, the first time. I really appreciated his commitment to his customers by taking the extra time to do things that way.
As for my trans. I bought a rebuilt foxbody mustang v8, world class t5 from a reputable builder. It has the shorter shaft, but on my build I did have to machine the end of the input shaft.
The stock t-10 has a little shorter length pilot shaft and the transition from the pilot bushing surface to the splines is a 90 degree angle. The t5 input shaft has a tapered section at the beginning of the input shaft splines, that and the longer pilot shaft made it so that the transmission wouldn’t fully seat against the bellhousing adapter plate. Once that was sorted out and the transmission was in, everything else was cake.
I used the stock speedo cable, clutch, and crossmember. I built a mount to mate the trans to the crossmember. I had a new driveshaft built as well. I bought a cheap short shifter off of eBay for around $14 shipped and figured out that a hurst stick for a 69 camaro was perfect to put the shifter knob right where I wanted it on a bench seat car.
With the stock 3.50 rear gear, and 275-45/ r18 rear tires, the car cruises down the interstate very well.
If you want to email me, I can send you pictures of my processes and parts if that would help you any. I’m happy to help get this kind of info out there to help you and others through this upgrade.