How many rubber shift boots???

I have a 96 x-cab 4x4 5sp sr5àI just had my tranny rebuilt and itÆs still having a faint whining in neutral, 1st & 2nd, and really faint in 3rdàit disappears when I push the clutch in while in neutralà

The tranny guys have their head up their a$$àthey seem the extra noise is from a missing shift bootà

What I have is the leather boot thatÆs connected to the console, and a rubber accordian boot, for 2 shifters (the regular one and one for the transfercase) is there an additional boot IÆm missing that would let the noise throughàI just want to make sure, so when I go back to them, I have more ammoàunder the 2nd boot, theres the big hole for the tranny shifters to come through. If there is an additional boot, whatÆs the part #à

I know itÆs in the tranny and they have to crack it open again, but this is their argumentàI told them if thatÆs the case I could just turn up my stereoà

IÆm thinking it has something to do with the input shaftà