I have not but it might be easier now to see what might be causing the vibration and can be done by just pulling the motor:
rubber bumper between the motor and the input shaft should be checked/replaced.
make sure there is the proper amount of oil in the transmission.
pull the input shaft and check the bearings. If the bearings seem worn try swapping in the input shaft from the rebuilt transmission just to see if the problem goes away.
Swapping the differential in an early gem is a bit of a process. You have to drop the front end so it will clear the battery tray. Email @Old_Houseboater for the service manual. It details how to do this.
I’d try the motor bumper first. From what you describe, that’s most likely the issue.
Also buy a tube of Honda m-77 moly spline PASTE and use it on the trans splines and motor coupler. Grease wont last very long so buy some of this stuff. This spline paste really quiets down the splines… Remember you owe me a beer when you drive your Gem and it much quieter.
It’s pretty straightforward. Disconnect the wires from the controller to the motor. If factory cables, they should be labeled so you will easily know how to reconnect them. There are bolts going through the differential into the motor attaching the 2. Once those bolts are out, slide the motor off the differential (be careful, it’s heavy). Use needle nose pliers to remove the old bumper in the coupler. Slide the new bumper in. Apply molley paste as @LithiumGods suggested. Put everything back together.
I’m in SD but I barely have time to work on my own GEMs these days. I’m happy to help a hobbyist here and there but maintaining a fleet is beyond what I want to get involved with. I’m also in the 2016+ camp. I’ve lost interest in the classic GEMs.
Have you tried Lalo? The mechanic that was hooked up with deep cycle battery store in El cajon? I can send you his contact info.