Neither of the wiring diagrams above use a 5V feed, everything is 12V.

Most I see for "kits" out there specify a certain speed for each to kick in. As we all know all driving situations aren't identical. So id rather have LU and OD kick in seperate, and not a time interval (one of the replies to my original request said "LU is 10 sec after OD kicks in" as an example) but I don't know if a set 44 mph or 50 mph is right for all situations either. Id like to have it vary based on amount of throttle input just like the current 727 does, and passing gear to work like it should.

The "specific MPH" is from using a fixed pressure switch. Again, 1 psi of line pressure = 1 mph WITH THE ORIGINAL REAR AXLE RATIO. Using adjustable pressure switches will tailor the speeds to what you want.

If I get the "50mph option" for OD and the "52mph" LU, what would happen if I were to punch it? Would it go from OD-3rd automatically, or OD drop to 2nd automatically, and if it went from 4-2 with drop down would it upshift from 2nd right to OD and LU all at once when I let off the gas? Id want a more natural progression of upshifts and down shifts than that.

When you punch it, vacuum drops, opening the vacuum switch and kicking off the OD and LU, if they're activated. As long as that switch is open, you've got a 3-speed auto with some extra weight on the back. After speed is above the set pressures and vacuum increases enough to close the switch, they will kick back in. With the 2 switch setup, If you're doing 70 in OD/LU and punch it, when you back off both OD & LU will come in together, but it's not harsh since you're not in the power. With the timers, you can set them so that the delay is there.