The tractor protection valve(tpv) is only for trailer lines. If you are keeping your truck as a straight truck and not running air to the back for a tagalong trailer you won't even use this system. The flipper valve and the red button are just controls to activate the tpv. The red knob should have a safety in it to automatically pop out and shut off the air flow when the pressure in the truck drops below a set psi. The flipper valve dosnt have that. The tpv is usually mounted Behind the cab and is what the red and blue trailer lines are hooked to. This tpv is what I used on my mack and has a built in safety (like the red knob) so the flipper valve would still be fine to use with it.
The air system is pretty simple in these old trucks. If you can find a nice simple diagram to look at its not bad as long as you don't over think it. (My issue).
I missed your one post until after I posted this. Personally I'd take everything out, figure if you want to keep trailer brake options, what style controls you want to use (either flipper or button), then start from scratch. Myself I think the air system was easier to figure out then the wiring was. When I stripped the old out of my truck some stuff still acted as it was hooked up but after following lines eventually they would just end with a plug.
I think I confused myself after reading this so hopefully you can decipher what I meant to say.