So I finally managed to scrape together some more time to get things on the 3A straight and I think I have cured my problem!� A big THANK YOU to RyanM for sending me another tower to tinker/compare with.� As it turns out, the shift tower was causing all my troubles.�
On my original tower, the cane appears to be worn out at the squared bottom and at the groove up at the neck.� This was allowing the cane to rotate some down at the shift forks "hang up" between gears....see below.
Here is the tower from my '47 and the original tower side by side.� I decided to use the '47 tower because it was in amazing shape inside.� The tower from Ryan is good also and I'll use it in the '47 rebuild.

Close up of the good tower..notice the sharp, square edges on the end of the cane.

Close up of the original tower.� The edges of the cane are very rounded off and the shift fork grooves are also not very crisp..

Here is the joint on the neck where I was getting quite a bit of rotation.� It was also just very loose and felt worn out.� While I havn't taken it apart again, I am guessing either the pin or the groove is worn.

Finally, here is the result of that wear in the cane.� When I was shifting from 1st to 2nd the cane was rotating in the neck and getting hung between the two rails.� This meant the cane was staying on the 1st-reverse rail and was trying to go back into reverse (hence the major grinding....

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Everything is back together now and I have put about 150 miles on the jeep.� What a difference.� I really can't describe the difference in how the jeep drives.� Before the rebuild, I had to "think" about every gear change (double clutch, RPMs, moving too fast, am I in the right gear, etc.) which made driving around the farm and town a pain.� Now, everything works like it should.� I can actually drive the jeep and really enjoy it without having to fight it all the time.
Was the rebuild hard?� I really don't think so.� The hardest part was knowing what parts needed to be replaced because I really didn't have "good" parts to compare them to.� The rebuild guides and videos are great.� I'm actually looking forward to tearing into the '47 t-90 when the time comes!
Thanks everyone!!!