I've got a 5 speed ZF behind the fuel injected 460 in my 93 F250 supercab 4x4. The only noise I get out of it is at startup, and it goes away shortly after I start the truck. Honestly, it sounds more like a throwout bearing than anything in the transmission. The clutch had been replaced right before I bought the truck, and no telling what they replaced (probably nothing more than pressure plate and disc).
Anyhow, I tow a 23' Reinell with 460, and 80 gallons of fuel, or a 26' camp trailer with 60 gallon water tank, as well as a generator, tool box, jacks, chains, firewood, chainsaws, and all the stuff I need when we camp, plus 40 gallons of fuel in the tanks, in the back of the truck. First gear is plenty deep for pulling from a stop, and I appreciate the heck out of that, as my other standard transmission'd towing rigs had four speeds with granny first that in essence were three speed trans' on the road.
We just bought an 04 Super Duty F250, V10/automatic, and I'm sorta torn between which transmission I like better. Both do well disconnected from the trailers, and out exploring on the two-tracks and mountain trails, but the constant gear changes make for a sore left leg after a long day of creepy-crawling around.