vibration after 3.23 to 3.91 swap

The tires and axles are the same as before the swap, so if they were not the cause before, then they won't be now.
Like you said, it doesn't do it in Neutral, so it ain't the engine,nor the TC nor the front half of the trans guts. . And it's only apparent in third gear at higher speeds....... so it has to be somewhere between the trans geartrain after the forward drum and before the ring gear. And the go-to guy is the driveshaft and/or the pinion angle.
Check the driveshaft run out., front,rear and a couple of points in between, as well as the the trans yoke bushing, for play.
In case you don't know, pinion-angle is the angle that the pinion centerline makes with respect to the driveshaft centerline. The smoothest running will occur when it is equal and opposite to the front angle, with all 4 wheels on the ground. But if you have soft springs, this will allow the pinion to wrap up undr power, to as much as 10 degrees depending on how soft and how much torque is input . This can snap u-joints. So to compensate, the pinion-angle has to be set to no more than about 2 to 4degrees higher than the front when under power. This might require up to a 7* nose down static setting to achieve....... and then under light throttle, there is nothing you can do about the vibration
Slapper bars or a pinion snubber can limit the wind up, allowing less compensation., as can stiffer springs.





I battled the same vibration with any rear gear from 4.30s to 5.38s . I cured mine by going to a 3.09 low gear in my A833 and putting the 3.55s back in. This gave me the starter gear equivalent of 4.12s but reduced my driveshaft rpm drastically.
Good luck