1986 mustang vibration

Ok guys i ve got a 1986 5.0 that ive had since new and has about 180,000 miles and heres whats going on.The car started to get hard to shift and i pulled the transmission and took it to a trans shop.While they had transmisson i stuck in a new king cobra clutch and had the flywheel resurfaced.After like a week shop called me back saying they stuck in a new main shaft supposidly and some misc little stuff they also stuck a new yoke on my driveshaft and balanced it too.Well i go back to shop and stick it back together and go to drive it and around 3800 to 4500 shifter shakes really bad,but if ur running it thru the gears with it flat on the floor and it passes that spot it smooths right up.If u come to a complete stop and just rev it up u dont feel a thing nice and smooth.I ordered this car since new and its never never ever gave me any problems i stuck a clutch stuck in it like 10 years ago still looked good when i pulled it out just couple months ago.Idles fine plugs are recent has ford motorsport wires its box stock like factory air fitler and pullies and such.i searched for vaccum leaks and notta.Double checked my timing,harmonic dampner looks fine.I pulled the serpentine belt off and took it for a short drive too still has the vibration so i pulled over stuck it back on to.Do u all still think its its in the transmission mmmm or what else am i missing that i should be looking at.Any help would be great too i figured maybe someone else has seen or ran into this before and iam new to site too.Thanks too

ok yes the shifter bushing is new the shifter itself is a old hurst short throw one thats been in the car for a long time.The shifter itself is the only thing i see the vibration in.The car is really smooth no shake in the steering wheel or the seat.Its like the shifter just get going crazy.I let another guy drive it and he said harmonics and he thought i should pull the trans and stick another one that i have on had to see if it takes the vibration away.i tried a second drive shaft and it still has it at the same rpm.He also said to me a bearing might be spinning in the case on the shaft and when the bearing gets a spinning the same speed as the shaft it stabilizes and it smooths out.Iam going to stick it up in the air on a lift and run it thru the gears and see what the drive shaft and all are doing its kinda a weird deal.The car has been really good to me and i learned something too i think i should have just bought a new t5 than to have this one fixed cause in the end about the same $$$$ but keep throwing ideas at me too