Yeah, that's what I'm afraid of.

Here's the best i can figure at this point, and why the EWD diagrams haven't been helpful.
The prior owner got a different dash loom, which also encompasses a good deal of the engine bay, too. Fuse blocks weren't available separately, they were part of the loom. My guess is your loom is out of a regular toyota truck, which is why the left kick panel fuse block doesn't have the connector needed for a 4Runner's rear components. Maybe they did it because of the transmission conversion, but others here have done the swap without having to fuss with the loom much. So not sure what the motivation was.

A few things bugged me besides the C,D,E,F connectors. The wiring laying on the passenger floor in your photo looks like stereo/speaker wiring, but it was coming out of the wrong area. on the 1987, The short mini-loom for the stereo and speakers branches off the main loom closer to the center of the dash, not the right kick panel.
This is kinda why I've been pushing to have all that aftermarket stereo wiring removed. It was just adding to the confusion.

Trouble is, I'm not sure what you have regarding the loom or ecu. The part number off either one would let me pinpoint it much better. Toyota does put the part number loom, but whether it's survived is hard to say. I'm not sure where on the loom Toyota put it. If it's in the engine bay it's surely faded by now, but if it's in the dash you might be able to read it. It's a white decal about 3" long taped right onto the loom. It'll have something like 82121-XXXXX.

The reason it would be nice to know what that harness was built for is if you want to wire that new fuse block into your existing loom it'd be helpful. Now, when it comes to wiring in that connector you should be ok, that connector was intended for that block. the tricky part are the wires coming from the engine bay and passing through the firewall, then into the fuse block from the top.

so i see a few options:
1) leave it be, with the back end of the 4Runner "hot-wired". not even close to my favorite solution, but the cheapest. Renders your EWD schematics and critical sections of the FSM useless, though.
2) try and wire in the correct fuse block to an unknown harness. Better, maybe not perfect, but what is. It'll be tough wiring in the section coming from the engine bay.
3) wire in that connector to your existing fuse block( the one already installed, not the one you just bought). See if you can transfer the circuit breakers over and wire everything in.
Not even sure option 2 and 3 are even possible.
4) Buy a 1987 4Runner intact loom. Extensive, but not as bad as it may seem. Will have the greatest cost initially, but in the long run, probably solve a bulk of your issues and save the most time. Especially down the road whenever an electrical issue crops up. And the dash disassembly is really quite easy once you get the sequence.
This one looks like the did a decent job removing. Maybe you could grind them a bit on price.Taking the dash out is much easier than it may seem, and will most likely give you a chance to correct other things.
ebay loom

What complicates everything is not being able to easily access the fuse block. You can unbolt it simple enough, but getting any slack in the loom passing through the firewall to make working on the existing fuse block will not be fun