I had a 95 with the 5 spd and 3:55's and now a 01. 5 with a 6 spd and 3:55's. IMO get the 6 spd. Both are identically geared in 1st and 2nd and 4th and 5th in the 5 spd is the same as 5th and 6th in the 6 spd. The additional gear in the 6 speed is added in the middle and makes for a more progressive application of power.
My experience with the 5 spd , both towing at low speeds/in traffic and crawling slowly around the mountains hunting, found me doing a lot of un-necessary shifting trying to find a comfortable gear. The extra gear in the 6 spd has eliminated that.
My normal shift pattern empty is 2nd to 3rd to 5th to 6th on level roads or 3rd to 5th to 6th if I have a little down grade.
You will get a lot of opinion about 3:55's vs 4:10's. My advice, get the 3:55's unless you are going to tow all/most of the time. I towed my 5er (about 15,000 #'s) almost 10,000 miles last year from the western mountains to the east coast and never felt the necessity for the 4:10 gearing. On a few steep 7 % plus grades I needed to shift into direct, but from Cheyenne, WY east I never had to shift out of 6th on the interstates. You won't see much milaeage difference between the two gear ratios (according to reports). My experience in two 1000 mile tests (about 90% of it towing) averaged 13. 8 and 13. 9 mpg. Driving empty at freeway speeds you will enjoy the lower engine rpm's )noise) with the 3:55's.