How do I wire replacement doors with power windows into the convenience box

Probably but I generally do a factory style soldered splice. Much less chance of problems.
Looks like the picture but then you slide some heat shrink over it and you have a good splice.

In your case you should only need one splice for the orange wire and one for the yellow. Then you need the splice for the grounds from the doors and the 4wd light.
As for how many, I've seen factory line splice runs with 5-6 in them. Far more than I would do though.
The problem becomes the amount of current the single run can handle. That's why they used the chassis for ground a lot. The chassis is a big hunk of conductive metal so you could ground everything to it. Then when computer controls started becoming very sensitive it was discovered that the chassis ground didn't work very well for the sensors. There was too much voltage drop through the steel to make them reliable. That's why newer cars have hundreds for circuits, every little item has it's own power and ground.

You shouldn't have. For the doors there should be one orange to each door and one yellow to each door. Those come back to the con. Center and join up at the connector.

Then you should have a 2 black wires from the drivers door that splices to go to the black wire in the connector as well. There should be one brown wire in each door, that goes to a connector that should hook it to the dash lights, for the lights in the switches.
The rest of the wires go from one door across the truck to the other door.

Check to see if you have power to those controls. You should have 12 volts at the yellow and orange wires if you have the fuses and breakers in the fuse box. The power mirrors are a different circuit in the con. Center. Just have to trace the power and grounds to be sure they are where they should be. Here's the mirror circuit. Different fuse and power connector than the windows/locks.

Yellow should be the window power feed, not locks. Orange is lock power feed. You need to track the wiring to see where the power actually stops, and make sure that the fuse panel is actually feeding those connections.

The first orange lead in this connector is for power seats. The second one should power the locks.

The mirror power isn't in this connector. It is in the next socket to the left of where this gray one goes.

Make sure to check the ground side as well. If you don't have a good ground they won't work either.