Mounting the master cylinder to the firewall does present some challenges. Mainly, the firewall would require extra bracing to be installed to prevent it from flexing. Using the under floor stock location would eliminate that, but I understand that the boosters will interfere with the shifter linkage.
Something you might consider, before you make changes to the truck, is get it in operable condition. Try driving it stock first, see if you like it that way. Sometimes the mindset of "you have to change it to be safe/make it drivable on todays roads" comes up, and people that are new to these truck get bombarded with sometimes false information. I'm not saying all the advise is bad, only that some of it goes a little too far. I will agree with going with a dual master cylinder, even though I still have the original style non-power single in mine. It's a bit of extra safety. Disk brakes? Nice to have, bot not 100% necessary. The original engine and trans? Bulletproof in stock form, plus teaching your son to drive a manual trans, especially a 3 speed column shift, will give him a one up on his automatic only friends. Thinking about it, even keeping the manual steering and brakes (drums only, go power if you go with disks) might even make him a better drive by making him have to pay attention to what's going on.
Whichever way you decide to, though, feel free to ask questions.
Fully understand it would be easy to go overboard on upgrades. Just trying to avoid doing it twice if possible. Take the brake system the way it sets. Being that it has sat for 10 plus years I'm pretty sure the master and all wheel cyls are probably shot. If not and a little fluid and some bleeding would get them up and going I definitely will start out that way and upgrade later. If we was building it for me she would stay manual and drums all the way around. Shoot I ran my Nova for decades with full manual drums reaching as high as 125 in the quarter mile, and switched to disc up front only when she jumped to 140 mph. Sand trap comes up pretty quick at that speed. Lol
You are dead on with making sure he can drive a stick. I try and teach him the extra things previous generations had to learn as much as I can. He actually learned to drive in a beat up old Ford Ranger with 5 on the floor. I would be a little more nervous with this one if it was 3 on the tree, but with it being 4 on the floor I'm thinking the manual steering will be the only thing he has to adapt to.
I have read about the brake boosters interfering with the linkage. Is that only with 3 on the tree ? Or also with floor shift models ?