Does this sound like a transmission problem?..

[Black87GT]

Ok, well about a year ago when i got my car back from a shop (ive been out of town since then) i heard a slight clunking noise, but payed no attention to it (i know stupid) and then let it sit for about a month, then i went to start it again and it was MUCH worse. The problem is that when revving the car i can hit this clunk clunk clunk sound or t-t-t-t-t-t for about 3 seconds, but after the revs are higher the noise goes away and cant be heard until you rev it up again. The noise cant be heard at higher rpms or idle, just when first revving it. Also it does this NO MATTER WHAT gear you're in, does it in neutral, with the clutch depressed, with the clutch out.. it does it no matter what. The transmission is a 4 cyl transmission i think (its a borg warner, has the smaller diameter input shaft, but has v6 writting on the top cover plate in like orange paint).
So does this sound like a transmission/clutch/flywheel/pressure plate problem or an engine problem?

I have taken all the clutch components and tranny out since ive been back and the clutch/pressure plate/throw out/ and flywheel were all junk (less than 1000 miles on them) and i have since bought a frpp king cobra clutch kit, and new flywheel and installed them, also just bought a new transmission and got it in but havent gotten to start it yet and im a little worried about it not being the transmission in the first place. I spent over $1000 on this stuff and im only 19 so if i replaced all of that for nothing and it turns out to be the engine ill be really depressed (lol).
I was told by numerous people on mustang forums that it sounded like a transmission problem surely because the noise isnt more consistent like it should be if it were an engine problem, but im not sure if it could even be a transmission problem since it does it no matter what i do with the transmission like stated above, i posted 2 videos that i took of the noise, so any help would be greatly and i mean GREATLY appreciated.

here are 2 quick videos of the noise.

first video at :57 seconds left the noise is present 3 quick clunks.

[ame="http://s280.photobucket.com/albums/kk200/Black1987GT/?action=view&current=100_0262.flv"]100_0262.flv video by Black1987GT - Photobucket@@AMEPARAM@@http://vid280.photobucket.com/player.swf?file=http://vid280.photobucket.com/albums/kk200/Black1987GT/100_0262.flv@@AMEPARAM@@vid280@@AMEPARAM@@280@@AME PARAM@@kk200/Black1987GT/100_0262[/ame]
[ame="http://s280.photobucket.com/albums/kk200/Black1987GT/?action=view&current=100_0263.flv"]100_0263.flv video by Black1987GT - Photobucket@@AMEPARAM@@http://vid280.photobucket.com/player.swf?file=http://vid280.photobucket.com/albums/kk200/Black1987GT/100_0263.flv@@AMEPARAM@@vid280@@AMEPARAM@@280@@AME PARAM@@kk200/Black1987GT/100_0263[/ame]

[97LaserRed]

DOOD! you need to take your car to a shop. you have so many vibrations, noises, clunks, and rattles you complain about. Its very very hard to diagnose a car over the internet/phone/etc. Im sure their are garages by your house you can stop by to have a licensed mechanic/technician look at it.

[Black87GT]

the car has had everything fixed except for this, i havent even posted about anything with this car in over a year.. if you dont like hearing me "complain" then dont read the thread.. i asked for a simple answer.