For some unknown reason to me the new battery is being drained?

Have you tested the charging voltage in the car with it running?

I wanted you to have the larger plug already unplugged, and see if you have the draw with only the 22 pin connector plugged in.

That way we know it has nothing to do with the large plug and we only have to deal with those few wires.

And yes, i'll get you a schematic this evening when I have access to that computer.
But the pictures will be big, so i'll have to email them to you.

With the engine running at idle and no accessories on, you should be seeing 13.5 to 14.8 volts. If it is not in that range, there is a problem with the charging system somewhere.

You need to do a voltage drop test on the starter system to find if there's a bad connection. Start by measuring the battery voltage right on the posts, not the cable clamps. Turn on the head lights so some current is trying to flow. You will find 12.6 volts if the battery is fully charged. Next, move the meter probes to the cable clamps. The voltage must be the same. If it is lower one of those connections is loose or dirty. Keep moving the probes down the cables and measure at each connection. The last connection on the positive side is at the starter terminal. Ford has had a lot of trouble with the wire strands corroding away under the insulation where you can't see it, right next to where it's bolted to the starter terminal.

Normal voltage drop testing involves having a a helper try to crank the engine so you can take voltage readings while current is flowing in the circuit. That will identify the cause of slow cranking. All you said is you have a starting problem but you didn't say what that problem is. If you have a no-crank condition regular voltage tests will find the cause.

You need to start a new question, and please be sure to list the engine size and mileage. Also include any tests that were done already and the results. You have a different problem. This question is a conversation between only two people. None of the other experts will see it or have a chance to respond. That does you a disservice. If you post your question within the next 30 minutes, I'll see it and reply. Otherwise I might see it tomorrow if no one else has replied by then.

If you want to start the testing, measure the battery's voltage while the engine is running. It must be between 13.75 and 14.75 volts. List what you find. That will determine where we go next.

I'd use a digital multimeter and make sure the battery has a full charge. If the battery is down, you can't do any testing. If the battery is down, get it recharged. Check charging system. After that, I can help you check for drain. Without a fully charged battery, your spinning your wheels, can't check anything.

If there is excessive amp draw, you pull the fuses, one at a time, till the excess draw is gone. An older way is to take battery cable loose, use testlite between battery cable end and battery post. If the lite comes on bright, there is a drain, you pull fuses one at a time, when you pull the fuse on the affected circuit, the lite goes out.