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

Do you have the correct wiring harnesses in the A pillars to plug the locks/windows in?
If not you will need to get that wiring and run it to the convenience center as well.

For the door locks and the windows you use circuit breakers not fuses, a fuse will blow very fast.
The locks get a twenty amp breaker in the Power ACC slot.
The windows get a thirty amp unit in the fuse block at the end of the instrument panel.

The harness runs from the door connectors inside the A pillars across under the dash to that box. It appears you have the harness plugged in. If you remove the kick panels under the dash on each side you will probably find the ends that the door cable connectors plug in. The cables on the doors normally have a rubber conduit with the cable bundles inside and the connectors sticking out. Run that through the hole in the A pillar (pillar door hinges are attached to) and plug them in. Add the two circuit breakers and they should work.
The images below are the center you show and the wiring that goes in them. If you note the rear view shows the gray connector as the door and window part, now you just need to find the other end.

Which connector ends can you not find? The convenience center end is there so the other ends will be taped in the harness somewhere. Most likely in behind those kick panels, but they may be taped under the dash. If the doors have the locks and windows they should have the matching ends. If not you will be better off visiting a salvage yard or you-pull-it and getting them.

You already have the truck side it is the gray connector plugged into the box in your picture, circled in orange. Just follow the wires and you will find the power window and door lock plugs which connect to the door wiring, somewhere along your trucks current harness.

If you mean the door harnesses, were they cut off? If so just visit a you pull it type place or a salvage yard that has that year truck and get the entire door harness assembly for each side.

There will be female versions of those connectors inside your truck. If you look at the length of them you can see they connect just inside the kick panels under the dash. Now you just need to dig them out so you can plug them in.

Was the picture of the convenience center block you posted your truck? If yes, the connector I circled in the other picture is the male end of the harness, the female plugs will be out near the doors.

You have the wires and connectors you need already. You need to find them. No other wires needed. That gray connector that is plugged in is the harness for the windows and locks.

The cable runs from that gray connector and will split off to each door. There will be the correct connectors there that the connectors on the doors plug in. Then the locks and windows will work. If you just "plug in" to other places you will not be able to use the windows or locks because the doors actually interconnect through that main harness under the dash. Good luck. Follow the wires and the connectors will be there.

Nope. The system isn't that complex. Basically switched powers and grounds. Window goes up with them one way, then the switch flips them to go down. Same with the locks. The window harness will have a couple more wires because you can control the passenger side from the drivers side.

OK the new picture says I'm wrong. You have the connector in the block but it looks empty other than one wire. If that's the case you do need the interior harness and I am very sorry.

You have two options, The easiest by far is to grab that harness from another truck, that will also show you where it runs. It's a common item though. The other would be to make a harness, but you still need the connectors which means you would still need the harness.

I'm sorry for the confusion.