A couple of observations from your descriptions and tests.
With only those two wires connected I can take my tester and touch the engine block and it lights up. The tester ground is touching the negative side of the battery. If I touch the engine block, radiator.... It lights up.
What happens when you touch the test light probe to any other normal ground contact? Such as a body panel, bolt, frame or anything other than the engine itself.
Unfortunately, a test light uses such a small amount of current to light up, you can get a lit light lit up (say that 10 times fast!) without much of a short. Is it a bright light, or dim?
And speaking of the old Black fused wire from the harness, just where is the old charge wire from the alternator? It's Black w/yellow and the same size as the fused Black wire at the relay.
This is the same if only one of those wires are connected I get a light up.
Meaning either one? Or just a particular one? If both/either, this leads to more questions than answers. Naturally...%)
Try disconnecting all the (4?) relays in the RJM section. If one of them is bad, you would possibly get some feedback through a short, or maybe there is a short between the Red and Black wires? Still hard to say at this point. Maybe Viper can follow the possibilities.;D
Now this may also be important. With only the single lead from the battery connected to the relay, none of the wires have power. If I touch either of the wires to the post, I now have power to the other wire, without it being connected. As well as "power" coming from the engine block.
So the starter relay seems to be out as a suspect for now. At least for any monkey business. Something going on in the new harness.
But just to be sure, with the positive cable still to the relay post, do you get a light if you hold the probe tip to the opposite stud (starter side) of the relay? What about the same test with the battery's negative side re-connected?
This would seem to indicate a short in the RJM harness. Either at the fuse block, or one of the relays perhaps.
Yep. Seems like it from here.
Normally, the Purple wire is waiting for a signal from the ignition switch. It should not have power on it's own, ever, coming back through it from the relay section, as far as I know. It's sole function, again from what I understand of it, is to simply tell the computer when the starter is engaged. I don't even think it's normally connected to any of the relays. I believe it is connected directly to the ECU through the harness. Could be wrong on that count, but someone can verify.
If that's the case, then maybe it's your ECU that is causing the trouble?
Also, I know why the starter turns... If connect those two wires and try to test the purple from the RJM that connects to the "s" post it lights up. So it's getting power even if it's not connected to the relay. If i take the two wires off the positive side of the relay the purple wire looses power. Now the red/blue wire that is supposed to send power to the relay is fine. It doesn't get power if the red wire and fused wire are connected.
Yep, the Purple wire is energizing the starter relay instead of vice versa.
If I pull the 15 amp fuse from the RJM fuse box, the red wire from the RJM loses power when the fused wire is connected. The fused wire from the original harness still sends power to the purple RJM wire when the fused wire is connected to the relay. This can with with the fuse pulled or not. This is also without the purple wire being connected to the relay.
Sounds like your fused wire (this is the large Black one with the tape on it, correct?) is somehow shorted to some other wires in the harness. You may have to peel back some layers (I'd do it no matter what at this point) to see what's going on in there.
At this point I don't think you have a choice but to see where each wire is going and what it's doing.
Getting back to the old alternator wire, if it's tied up inside the harness without being safely capped off, it could cause all this. After all, it's simply the other end of the fused wire, so would have power any time the fused wire is connected to the battery power.
See if any of that makes sense (it's late for me) and if still a mystery, just start digging into the wrapped sections of harness and straighten out the inevitable spaghetti factory underneath.
And I think (unless otherwise instructed) that you would do well to re-connect the battery negative to the block and keep your full grounding schemes in place during testing.
Sometimes a test light is fine, but often during this kind of testing a volt/ohm meter works better.
Good luck.
Paul