I loved my '66 in spite of the "special options" it had such as ventilated floorboards and intermittent brakes. When I got it it had the factory 3 speed hooked up to a 283 Chevy but converted from column shift to floor shift. The shift pattern was upside down and backwards to what it should have been and in spite of having grown up driving manuals I eventually stripped out 2nd gear and converted to automatic.
While manual may be more fun when your young there is a lot to be said for the reliability of a TH400, especially one that has already been rebuilt. In '66 Jeep was using a Hydraulic clutch, which was awesome! but was also capable of bending the clutch actuator rod in certain conditions (guess how I found out
I will join in on recommending brake upgrades for no other reason than the '66 came with a single reservoir master cylinder which came very close to causing me to cause a major pile up in heavy traffic when a brake cylinder failed leaving me with no brakes at all. I'm not opposed to drums but am opposed to single cylinder brake reservoirs.
If he really has his heart set on converting to a manual I doubt it would be all that hard to find the parts, I see hay more manuals than automatics in the Kaiser era Jeeps. I'm not sure difficult it is to find the bellhousing (assuming it's a 327) I have a friend in Michigan that has had his '68's engine (Buick) in pieces for many years just because when he starts getting ready to put it back together he starts thinking how much he doesn't like driving stick any more and other things become the priority.
Just some thoughts.
I wish you and your son well with this new truck, I'm sure it will be a great memory maker.