The pedigree looks off. Sounds like a case of buyer beware. Don't forget, 5 speeds have far lower resale values vs. automatics in any given vehicle. There may be a $1,000+ difference even in resale values.
Carfax.com reveals some info, what I don't know:
Year/Make/Model: 1999 ISUZU TROOPER S
Body Style: 4 Dr. Wagon/Sport Utility
Engine Type: 3.5L V6 DFI DOHC
Manufactured In: JAPAN
Search Results: 5 records found in our database
IMPORTANT! The 5 records on this 1999 ISUZU TROOPER S will confirm a clean history or uncover potential problems. Find out by ordering the complete CARFAX Vehicle History Report.
So the manual isn't faster. I doubt if a mileage difference would be noticeable on these rigs. The only area that a manual has left to excel in is engine brake, which not many people use/need in the first place. A manual is probably better for descending steep hills, but an auto is better for ascending steep hills. The automatic's reverse gear is a little too high for my taste. I wish it were lower, but if I really need it to be lower, I just throw it into low range. The auto is pretty much bullet proof, and I presume the manual is the same.
The thing about the newer automatic trannys is there is no dip stick. Even when they did have dip sticks, you had to drive the Trooper around in order to check it as per the manual. I say go for the auto.