Summit probably says they are the same transmission used in the '95 Cobra R because the TKO and 3550 are the same design, just with stronger components inside the newer transmissions. The original 3550 has weaker gears and smaller output. Also, the input is a comparative weak spot on the original 3550.
The 3550 uses brass blocking rings (same design as the Top loader), but they have carbon friction lined blocking rings in the newer TKOs for better high RPM shifts. You can buy the TKO parts and put them into a 3550 - the two transmissions are that similar. That's why I would be surprised if you have trouble finding 3550 parts, TKO parts can go in there. Of course doing one gear here or there could be an issue depending on ratios.
I considered replacing the input and main shafts with TKO parts to strengthen my 3550, but it's expensive and the other internals still aren't as strong as a TKO. You can replace all that, but it's probably better to just go with a TKO. I pasted some info from Hanlon Motorsports below from when I was discussing upgrades with them last fall. I hope this info is helpful.
the 3550 trans was rated at 350 ft lbs tq even if you upgrade the input shaft (169.00). You can upgrade the output to a 31 spline (279.00) and we can bore out the tailhousing (50.00), buy the yoke 89.00 and the rear seal 15.79 and the tailshaft bushing 12.59. The carbon lined rings are 75.00 each and most guys put them in 2-3-4 gears ( you can do anyone you want) upgrade to the steel shiftforks 1-2 79.00 and the 3-4 59.00, this will help HP wise, BUT you will still have the weeker gears in it, so depending on how many miles on the tranny and how it was taken care of depends on what you can put thru it. Getting an older TKO, you will still have the same gears as your 3550, so you are in the same boat. We do sell new TKO 500 2095.00 and 600 2195.00 including shipping.