Will a 4T65E HD work in place of a 4T60E? Not typically, you would need to swap computers, wiring, and it would simply be easier to find another 4T60E, or go for a rebuild.
Now, here is the interesting part. The '94 Ultra has a 4T60-HD, not a 4T65E-HD. You will need to swap things over, but I don't believe that it would be that bad. Going from 93 to a 94, you have a different computer system setup, so you may need to move the wiring harness over, and the 4T60E and 4T60E-HD are a little different, with items including differentials, and final drive ratios. I would expect to swap harnesses, as well as one of the drive axles (passenger side I think), and I think the computer may need to be tweaked so that the speedometer isn't funky.
I am by no means an expert, so I will let one of them chime in.
It might be fun to simply do a full drivetrain swap.