Whine From Transmission? Please Help!

So i bought a 95 Cobra and it had a slight whine that sounded like it was the trans or possibly in the rear end. i took the car to a garage to have it looked at and i was told the rear end was bad and the output bearing on the trans was as well

so i spent around 2k on a rear end rebuild which covered everything bearings limited slip diff and ring and pinion. when i picked the car up the whine had gone from slight to the loudest thing ive ever heard the noise was still a whine but when from low pitched a semi quiet to the point where it over powered the sound of the exhaust.

so my mechanic that rebuilt the rear end told me the trans was most likely bad. ok so i bought a trans but i was tapped out so i picked up a t5 on craigslist and put her in myself. i just got the car down off the jackstands i take it down the road and i still have the same whine not as loud as after the rear end rebuild but louder than it was when i first picked the car up

so did i get sold a bad transmission by some ******* on cl? id like to think not but possible or did my mechanic jack up my car? any input or past experiences from you guys is much appreciated. i paid 5400 for this thing and im already into it for almost 9k with all the repairs and parts. PLEASE HELP! i just want my pony to gallop again:-(
 
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Did you use Ford parts or the the ones from the parts store because I had the same problem with the ones from the parts store but then I got the Ford ones and it stopped for me
 
throwout bearing is from ford racing i ordered a ford racing pilot bearing and it didnt come in time so my mechanic said he had a few lying around and it wasnt a big deal cause theyre all essentially the same. so yes in the t/o bearing and im not sure what he used for the pilot
 
Just with a T-5 it seems to me everyone I have ever really got into has some sort of a wine to it. I know mine I have now does whine a little as well but I have heard its kind of a normal thing for the t-5 if you run synthetic transmission fluid like I do. Now when I run normal Transmission fluid I don't really hear the whine.
 
no aluminum drive shaft. and the trouble im having is it has a slight whine with the orig trans then i had the rear end rebuilt and the trans fluid changed and then is sounded like a bandsaw (so loud the trans drown out the exhaust) so i bought another trans put it in and once again this one whines....brian you mind if i email you a video of it so you can see what it sounds like?
 
T-5 whine is pretty common, but not normal. The internal whine most often occurs when a trans is run with incorrect fluid, or run low. It is possible to replacing a whining T-5 with another one.

Shifters can also create a whine noise, FYI.

But, just because ons has an aftermarket shifter and T-5 doesn't mean whine is to be expected. In my Fox, with a T-5 i rebuilt myself, with an MGW shifter and an Al driveshaft...it's virtually silent. You can hear minor whine with the radio off and windows on.

But back to the OP...Is the whine constant? Does it increase with vehicle Speed, or engine RPM? Is the whine the same in all 5 gears?
 
well guys the neighbor poured diesel fuel in my gas tank and i ran the car so now its super dead...luckily its covered under vandalism on my insurance but i do not know yet weather they will total it out or give me a check to get a motor...ill keep you all posted.