Wheel balance / vibration issues occur at different speeds and at different temperatures. As the tire heats or cools down, the PSI changes and this can influence the tire balance or make flat spots more noticeable.
If you replace transmission, have them replace transmission mount, flex-disc, center loop (where the two dive shafts are joined together) and differential mounts. Short of the axels, this take care of every rotating part past the engine. Except for the differential mounts, all of this stuff is coming off anyway, so replacing them doesn't add any labor cost, just parts.
Also, have a friend idle the car at the various RPMs where you know the vibration kicks in. While he/she is idling the car, put your hand(s) on the engine (like the plastic covers over air filters & wear gloves!) and see if you can feel a vibration with the same frequency/characteristics that you're feeling while driving. If you do, but you don't feel the vibration in the cabin or steering wheel, then know at least the motor mounts are doing their job. Likewise, it is something past the engine which is magnifying the vibration while you're driving.