thanks for the better pics man!

First circle- T shaped connection. Alternator connection. Find the KA alternator, get a plug that plugs into the KA alternator. You will need to remove the T shaped plug and splice in (solder) the KA alternator plug (which is oval). When you get the SOHC KA alternator plug, take a pic of it and put it up, I'll tell ya what exactly to do, its real easy.
Second circle- beneath the first- rectangular plug- goes on the transmission, IIRC its the plug for the neutral safety switch, which is on your trans, pretty much regardless of year or trans type- they all used the same sensor.
Third circle-far right, lower- is this part of KA harness or S12 harness? Is this part of the harness that goes to the trans? Is this the same connector thats in the second to last pic that I'm asking the same questions of?

You got it chief, ground that bitch out, but make sure to clean the metal to bare before installing so its a clean connection. Then, paint over or cover with liquid electrical tape, to prevent corrosion.
The other circled plug, the 4 pin circle connector, is for the cruise control actuator, which your car doesn't have apparently. all cars, regardless of cruise or not, have this plug, its just not used.

This is SO close up dude, its hard to see. Back out a bit and reshoot, noting which of these pics you are reshooting. I'm thinking, just because of the colors and apparent location, that these are for the AC compressor and power steering pressure switch, but I could be totally wrong, so zoom out a bit and post that up as well.

This should plug into the KA engine harness???... thats how the DOHC model is set up anyhow....

These are your old coils. Forgive my stupidity about the sohc model, but the coil might be in the distributor on this ka, but I need to do more research. IF the coil IS in the KA distributor, you can remove the stock CA20 coils from the car.

I'll let the other KA guys handle this, I think one of them said it was for the brake booster.

Engine grounds, connect them to wherever screw/bolt they rest by naturally, AND CLEAN the surfaces they connect to! you really want good connections on these, as this is where the ECU grounds thru, all engine functions more or less ground thru these two screws.
The circled connector in the pic there,... looks like it would go to the distributor in the front, IE same style connector. Does it reach comfortably? Or is it right near the idle control motor assembly, any familiar connectors there?

Same circled connector as before pic, correct?
One is your fuel sending line, one is the fuel return line. You have one of the fuel lines hooked up. MAKE sure the the fuel line
coming out of the filter is hooked to the
lead that goes to all the injectors. Make sure the lead that comes out of the bottom of the fuel pressure regulator goes to the return line, the one w/o the filter. If you are unsure which of the lines in the car is the fuel filter line, the fuel sending line, turn the pump on and see which one has gas coming out of it. be careful tho, lol
The large line is *probably* a heater core line. I'll wait for a sohc ka guy on that one.

That looks like one of the engine connectors.
Dunno if you've figured this out, but the engine harness maintains its shape after so many years, IE it forms to fit. At a certain point, you should be able to just set it on top of the motor, and all the connectors will line up *about* where they actually connect onto the motor. The plastic hardens from heat and age, and things just set up the way they sit, so you should be able to use this to help you. A service manual would help too...

Thats the lower connector that is circled in the first pic, right? its on the pass side strut tower, next to the fuel filter, apparently? Is this part of the KA harness or S12 harness?

Looks like one of the coil wires???
You know, I'm actually kind of wondering... You do have the KA ECU harness, right? I mean, if thats the CA20 harness, its NOT going to work with the KA. I wasn't sure if you were aware of this or not, and we'd go in circles if it was the CA20 harness, lol