Don't cheap out the tow on the tow package and the ambulance package (dual alternators). You will be happy you have it in the long run. The GM product is superior to the others in the long term.
I believe they make the NV4500 with different 1St gear ratios . This may also be available for the 5600 also. I hope some other member can verify this.
Water in the fuel? Do You use the fuel source for other trucks/machines? Sounds like you sucked some shit into the injectors! May have to disassemble injectors or send them out for cleaning. :( the filtering have let debris through.