Ok, say the engine is a gen3. Which means different ECU is needed, wouldn't that mean that now, as it sits, it would run rough all through the rev range? Because it sits nicely on 1000rpm if you're holding the throttle every so gently, but as soon as it starts to drop below 800ish, it really struggles and stalls. But anything above 1k rpm and it revs up beautifully.
 
Thanks for the confirmation, arty.
 
This means the CPU should be fine and the AFM is still necessary?
Then it's most likely a vacuum problem like I thought?

I think there is still some confusion here - just because its a 1993 motor doesn't mean its a Gen 3. That's clearly a gen 2 in your pic.  
To answer your question, YES, it would run like a pig (rich) everywhere IF it was a Gen 3 wired to a Gen 2 ECU, because of the 550cc injectors not 440cc.
 

• Yes, you will still need the AFM (not as bad as what people make out).
• Yes, its probably a vacuum leak somewhere. 

BTW: that's some funky looking BOV - maybe that's leaking?

It's quite possible the BOV is leaky but it worked fine on the other engine, and yeah, have established it's a gen2.
 
I will be replacing the BOV with the stock plumb back/return one asap, maybe I should just grab one of them and see how it goes straight away? 
 
As far as checking for leaks elsewhere, should I pull a hose, block the other end and put some pressure in it, and comb the whole thing with soapy water? 
 

Yeah it'll be worth fitting a stock BOV/BPV just to make sure. 
Yep soapy water around the connections will definitely be a good idea to check.

Checking for leaks, yep... that wouldn't be a bad idea.... but it will take a while.

It is definitely a Gen2, as mentioned previously.
the 93 Gen2 though STILL has a different pinout to the 90-91 ECUs. Unfortunately, i've already sold my Gen2 ECU.

 Ok, so that first image didn't help much given the situation.
Here's another image with a more thorough breakdown of ECU part numbers.
Your original engine was 
SW20 I(JP)
 
the new one is 
SW20 II (JP)

You should be able to confirm that with your existing ECU part number. The other one, will be harder to confirm.

People, correct me if i'm wrong.

 

ok, i just had a proper good look, and apparently I had it wrong all this time. It's a 1991 body, though I know it won't change much.
 
Can't confirm the SW20 I (JP) or not, but I'd be confident in that it is. Says nothing about it on the ECU, but I didn't check numbers.
 
Another Idea was that when checking the cold start injector thing, it read about 4.6ohms. My other engine was sitting on like 5.7ohms. A friend (Who posted/asked on ae86dc.com) mentioned that if thats wound down too far, it starves it of air, causing it to stall. If I adjust the 93 engine to suit the same ohmage as the 91, would that have any positive affect? Or is it better to just ignore that and go get an ECU? On that note, it says in the BGB that it should read between 2-4ohm. Why is it so much higher to start with?
 
If that option, should I go a nice aftermarket ECU? If yes, any suggestions?
 
Also, I really really do appreciate all the help you guys have been able to offer here. So thanks for taking a bit of time out to write some stuff down for me. The cars been off the road way too long for my liking and sanity, and it will be great to get it running again soon. : )

Here is food for thought. Have you checked the throttle body sensor voltage when the throttle body is closed? This could also have an affect on the idle of the engine. There is an adjustment screw which enables you to twist the throttle body sensor, similar to distributor. Thats brings me to another point, have you checked the timing of the engine to ensure its correct? You need to get a wire and join 2 pins in the Diagnostics panel to set the engine to 10 Degree's, then using a timing light twist the distributor until the timing light shows the engine running at 10 degrees.
 
I can't remember if its on the Gen II or not (It is on the Gen III), but there is a little screw that adjusts where the throttle closes on the throttle body. I.e you can set the throttle so it sits slightly more open when on the return spring.
 
I wouldn't worry about a new ECU at this stage, you'll probably run into the same problems. The Toyota ECU is very safe to use to resolve these issues prior.
 
Have a look at these things, it shouldn't take too long and may fix your problems. 

Yes that screw is on the Gen 2 as well.

Check those things, have a look at your ECU part number... match it with one thats listed in that picture and go from there.
Also, with the diagnostics bridged with a paperclip or wire (as PETE mentioned), see if it idles.
What that will test, is whether the engine is capable of running with all of its sensors at BASE ignition timing. 10 degrees.

Do you still have the other engine?
All of the physical components of both engines will be the same (well... near enough)
you could compare or swap out sensors if you wanted to. Just bear in mind that the TPS will need to be adjusted properly if you do that. 

Ok, so on Tuesday it was still not idling at all. Would drop below 1k rpm and die. I went away for work for 3 days (Got back tonight) and had a mate come around. We were gonna have a look at some ideas posted here.
 
I decided to just try and start it and see how it went.
Somehow it just idled fine. Absolutely no problems. Revved up fine and everything. So I took it off the stands and went for a drive. Got halfway down the road and it died!
Pulled up the engine lid and saw the damn BOV had fallen off. I guess I forgot to tighten the **** properly.
So I rooted around, trying to find a 3mm allen key, and tightened it up properly. Hell yeah!
 
So in the space of 3 days, it just magically fixed itself. I have no idea how or what happened, but my car is now on the road.
 
So a big thanks to all the help posted here. Cheers guys. I'll see you on the roads soon!