Take some extra time, spend some extra money, and while you are rebuilding the tranny have short 5th and 6th gears installed. you will love them. Here are my comments from a previous thread:
"Let me add that in addition to shorter rear end gearing (I have 3:55) if you ever have your transmission apart for any reason take the time and spend the money to have shorter 5th and 6th gears installed. I have an 0.80:1 5th and 0.64:1 6th and they make for nice even steps through every gear from 1st to 6th. AND top end is now in 6th where it should be instead of 5th (redline in 6th in my car would be 200 mph so real V max should be right in the heart of the powerband). I can even use 5th around town once in awhile if I want to calm the car down."
I too blew up my input shaft and when I had the tranny rebuilt the tech was eager to show his skills (he had to machine a few thousands off a shaft to get it done) by doing the shorter top gears. Cost $1,000 extra. The gears come from the Aston Martin/Jaguar version of the transmission. Guy who did it is Alger at a huge transmission rebuilder named Alltrans here in Phoenix:
All Transmission Parts
1333 North 21st Avenue
Phoenix, AZ 85009
(602) 252-2614
I'd recommend them for a standard rebuid also. They always have a Viper T56 in stock. Price was $1,550 when I had mine done awhile back. They did the install for me for $400 so the whole rebuild with short gears cost $3,000.