help..installed gears and clutch and have a vibration now and a whine!

so my so-called mustang expert friend and i installed a new fms heavy duty clutch and a set of USED 373 gears ...one thing is clear..we used the original shim size and it was not sufficient to prevent the whine..also the rear diff gasket leaked and ive driven it for a month or two low on oil...also...when i just put the car into gear and accelerate there is a clicking/snapping noise from what sounds like the clutch area cuz i can feel it in the clutch pedal but it goes away after 5mph+...today it seems that my car has started to vibrate immensely from the trans/shifter above 2000k rpm and sort of growls a bit... i've read previous similar posts so i'm wondering..what are the chances it is the incorrect pinion gear depth or maybe the driveshaft was bolted into different holes than they were originally..could it be my pilot bearing which i didnt replace? i did have to use the bolts to pull the trans onto the bell housing but i would think that if i messed up the pilot bearing doin this...it would vibrate immediately and not 2 months later...i am goin to replace the gears with new ones this week but this is all i can really afford...is my input shaft possibly in jeopardy?..i really really dont want to take my trans out and waste my time when i dont know what to look for and i dont wanna pay someone for all this cuz im nearly broke..i need some help guys

nah i didnt mark the driveshaft but the vibration has started to occur 2 months after i did the install..if it was the driveshaft...i would have thought that the vibration would have occured immediatly after the install, not 2 months later

i didnt have the flywheel resurfaced but i knowthe sound of a chattering clutch..its not that...and i heard a new noise again today that i could feel in the shifter and the clutch pedal...its was a clicking noise that went in unison with the speed of the car as it slowed down..ie- as the car rolled to a stop, the clicking got slower and slower until i stopped...could that be the fact that i am using the stock self-adjusting clutch cable or is it something bad like the pilot bearing...as for the gears..im having a pro do them on monday but i dont think thatll fix the clutch noise/vibration issue...the whine will be gone but im afraid im gonna wreck my new clutch or trans input shaft or something...anyone have any experience with these sort of problem noises?

ok, so $370 later i had my gears reinstalled by a pro that used the pinion depth tools and such so my gear whine is gone completely which is nice....but the vibration in my trans is not...i am starting to think that the pressure plate has come loose and out of balance or something because there wasnt any vibration when i first installed the new clutch..it started to happen a few months later...we didnt use lock-tite on the pressure plate bolts but im not sure if youre supposed to....being that i can feel the vibration when i rev the motor in neutral leads me to believe that the driveshaft is not in the wrong position and also a driveshaft problem would have arose immediately after the clutch install...should i take the trans out again and look and see if anything is loose...this i such a pain in the ass to do and im not convinced the problem wil be readily visable to me... or should i take it to a pro just to take my trans out to check and see if i did everything correctly..for a few hundreds dollars i dont have to spend...also....is there any chance that because i am still using the self adjusting clutch cable that the clutch is not totally disengaging when my foot is off the clutch pedal and in neutral thus causing the clicking noise that goes the same pace as my rpm's..i bought a new adjustable clutch and its in the mail but i cant keep throwing money at the problem