Hat's off to Sierrafery for all the efforts he is making to diagnose this problem at a distance. But he did say, and I think this might be hugely important, that it is essential to check the EARTH POINTS. We have all seen cars on the road whose brake lights light up when the indicator is supposed to be on, or similar faults. This is usually an earth fault. This might also account for why you have the same faults with two different fuse boxes.
Failing that, I would be tempted to find where all wires have been cut and then reconnect them, to the originals, i.e. put things back the way they should be from manufacture. In the process removing any extraneous wires added by the bodger.
Any faults that are in the system then should be diagnosable and mendable. If you cannot find, by visually looking for them, where the cables have been cut, look for wires with the same colour indicators in them, i,e blue with a white stripe or whatever, using a wiring diagram to ensure that one end of the wire should be connected to the other end of the same wire, and not to any others. Then disconnect, the battery, pull all the plugs and test each wire individually, from pin to pin. If for some reason you cannot get to the pin, stick a needle through one end of the insulation in a wire to touch the copper core, then if necessary, do the same at the other end of the wire. Then put your meter to "resistance" smallest reading and touch the two probes to the two needles. This should show no, or a tiny, resistance if the wire is whole, i,e, connected, not cut. If you get no reading then you know the wire has been cut and you can search for the cut or break. Once you have found all the cuts/breaks, mended them and insulated them, you can then put all the plugs back in, reconnect the battery and go from there. If you can only disconnect the plug on one end of the wire be aware that each test is connecting one end of the wire to whatever else it is connected to.
By the way, do not forget that where a wire connects to something in a door, it has to pass through the gap between the door and the door pillar. Here the wires have to bend and although they are protected by special insulation, it is a weak point. Relatively easy to check though, just pop the fat insulation that covers the wires between door and post and check each wire very carefully.
What I have just told you is unbelievably basic as I am a real novice at electrics, but I get the feeling that is where you are too, or am I am wrong?
It may be time consuming, but if you take it logically and methodically, and go for the wires to the problem areas first, you will love it every time you find a cut or broken wire and fix it, even if all you use is a choc-block just to begin with.
Also, check to see if any wires have crossed, worn through their insulation near another one, or if connection pins have bent and are touching. If it was me, as pairs of items have a problem, I would start by taking the shrouding off the steering column and looking all around the stalk switches.
You can also check to see if a wire has a short to earth, simply find a good earth point then put one probe to it and the other to a terminal pin on a wire or as explained before, to a needle in a wire. If you find a reading indicating a connection to earth where there should not be one, then you need to inspect that wire until you find where it has accidentally made a connection with earth, through a grommet for example.
Even if you cannot find the fault, then, if the proper wires are all connected properly, then you have got rid of the botches and bodges. So proper procedures by an auto-electrician should be quick and easy.
This is time consuming and a bit of a pain, but as it seems likely that the fault is going to be something like this, then what you have that is free, is time. Or you pay another guy to do this.
Sierrafery or another member with more electrical know-how than me might have a better idea. I'm sure they will jump in and say so. I am sitting here waiting for any ribbing I might get!