possible issue with bearing preload causing vibration. when the gears were changed was the case spread set correctly, and was the crush sleeve replaced and the preload on the pinion set correctly?
a lot of people just swap out gears and tighten things down till they think it is tight enough. there is more to it then that.
A lot of transmission shops that work on these don't even know what they are doing. most are familiar with setting up a chevy rear end which is very different from a ford setup.
The biggest mistake most transmission shops make is they reuse the crush sleeve on the pinion. a crush sleeve can only be used once, if you overshoot the torque spec on a crush sleeve, you have to take it all apart throw it out, replace it with another new one and start again. usually they will reuse a crush sleeve, torque it lower then original spec, and call it a day. 50 miles later the pinion shaft starts dancing around and you start to get all vibration noises at speeds over 35mph. the dancing around then basically ruins the gear set and the bearings.
additionally aftermarket gear sets (replacement gears) have completely different backspacing then OEM gears from 40 years ago. a lot of shops just assume the aftermarket gears for a ford 9" are manufactured to OEM spec. they are not, not even close usually. so when they do a gear swap, they reuse the same spacer on the pumpkin and then loosly setup the gear mesh that they can never get right because the spacer is now incorrect, they just get it close and call it a day. on a chevy the spacer is set on the pinion shaft, on a ford there is a spacer gasket that must be changed between the nose of the pumpkin and the body of the pumpkin. it can get involved because you need a spacer kit that is a special order and then unless you have a calibrated spacer tool(OTC) which is VERY rare and impossible to buy new today you basically have to setup the gears, see how they mesh with the grease and take the entire thing apart replace the spacer, reset the backspacing on the ring gear, reset the case spread and start again.
this eats up HOURS AND HOURS of labor for a transmission shop so they basically screw the customer and throw the chunk together and hope the customer doesn't notice the new noises from the rearend.
this is why there is a big market for Used OEM pinion and ring gear sets. ford setup all the OEM gears with the same spacing, so this allows a much faster swap where you can reuse the same spacers and come inside spec. the problem is a good used set in a specific ratio might be impossible to find. after 40 years not many matched pinion and ring gears set survive. many ford gears are also timed or lapped matched so you cannot mix and match from 2 sets of gears they have paint markings showing the proper keying of the teeth.
All that said there could also be issues with the U joints on the driveshaft. but if you have no issues before the gear change and now you do the problem is in the pumpkin.