Drivetrain Transmission: 3550, Tko Or 3650?

Hi All!

I just purchased a 2003 Mustang GT project car a month ago or so. I knew it was going to need some transmission/rear end work when I bought it. In 2011 the transmission had been replaced by a local shop and so I took it back there for them to look at it. They said it needed a rebuild and I questioned that as it only had a few thousand miles on it since the rebuild and the counter guy says that the previous owner must have abused it and pulled the odometer cable to stop the mileage from going up. So I had them "Rebuild" it. I got it back in the same state, 1st, 2nd and 3rd whine really bad and 4th and 5th sound like marbles grinding. If you get on the gas it sounds like marbles grinding in any gear. So I got the previous owner to give me the facts on it and he says that it sat at the shop for a year as he didn't have the money to get it fixed and that they are the ones that changed out the transmission in 2011. The reason I say that is it has either a 3550 or TKO transmission in it and not the 3650. I can't tell exactly what as all I can see on it is "MSK-11734" stamped on the drivers side of the trans. The Shop is saying that the previous owner must have changed it out somewhere else. I asked the shop what rebuild kit they bought and he couldn't answer me, he was going to have to ask the tech. (what?!?!). I've got a 2 year 24,000 mile warranty on this trans so I'm kinda stuck as I've already dropped 1k on the rebuild. There going to fix this or I'll take them to small claims court. The previous owner says they are the only shop that worked on it and the reason there's no mileage is it sat for the last year and a half.

So my question after that novel is should I keep the 3550/TKO or have them put a rebuilt 3650 in it?

Thanks for reading!

Mods:
New .373 Ford Racing rear - Complete rebuild this week.
AccuFab Plenum
75 MM Professional Products throttle body.
BBK Cold Air Intake.
Lowered, unkown springs
Pro Stop slotted rotors.
 
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