Fuse box under the hood has power w the ignition off

I have a 2001 mustang GT with an automatic the previous owners apparently headed for 6 months off of car lot and the car broke down he had it towed in and they told him the mechanic shop that the wires are reversed on the alternator so the wires were reversed on the alternator and it turned up some wires on the harnesses not too much but I replaced harnesses,I replaced the fuel injector harness and the fuse box harness the ECM and the gauges and what's going on now the fuse box is staying on all the fuses are lit up under the hood and the dash is coming back on the gauges are turning back on with the key off and odometer shows lines going through it the traction control button light is lit up I can't read the computer from my code reader and it kills the battery I heard about your back up and it runs fine like a raped ape so just to recap I replace two harnesses fuel injector harness it goes to the big plug underneath the hood the fuse box harness the ECM and the gauges seemed like it worked at first for about 45 minutes. and then went back to doing what it did
 
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All of the fuses in the Battery Junction Box (BJB=F1) are supposed to be "always on" power.

The fuses in the central junction box (CJB=F2) can be "always on" or on in various conditions depending upon function.

IF the cluster is on with the key on, THEN we need to know IF fuse F2.34 has input power or not with the key off.

What to do next depends upon this test result. But basically if there's key off power in fuse F2.34, trouble shoot an ignition switch problem.

If there's no key off power in fuse F2.34, then suspect a CCRM problem. We need to know IF there's key off power in F2.2 and F2.8.


1999-2004 MY fuse panel schedule:

1996+ Crank with no start check list
 
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I'll be getting up and moving around soon I have to go out there and check it out appreciate your response I've been working at this for about 2 weeks if not more had a guy come out and put a new used ECU In-and married the gauge together about 45 minutes they went back popn on I about 5 min.after you shut the car off I can't get my code reader to link with a car and like I said it drains the battery connected I will check those fuses I will get back with you not too sure about what fuses where and which one is what but I'll figure it out
 

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I will check those fuses I will get back with you not too sure about what fuses where and which one is what but I'll figure it out
Just wondering why you need to figure out which one is which as I gave you a link to the BJB=F1 and CJB=F2 fuse panel schedule.

1999-2004 BJB CJB fuse panel layout:
 
I'll be getting up and moving around soon I have to go out there and check it out appreciate your response I've been working at this for about 2 weeks if not more had a guy come out and put a new used EC
I'm trying to get a folder together to send you all at one time I'm not too sure about this electrical stuff so I'm taking some pictures I just need to get it together for you I'll send it thank you so what the key off under the hood everything was lit up every fuse with key off same thing it have 12.30 amps when it was on and off I tested the battery and then I tested the fuse box negative battery post to a fuse and it was the same 12.30 now under the dash there was quite a bit of them on with the key off and even one 20 amp fuse was blown I took pictures and asked if older I'm going to send you
 
If I had an email that could be a little easier to send these pictures and understand there's a fee for the services I'll pay it
 

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I only have a few more to send
 

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The fuse box under the dash I only did it with a key off
Just wondering why you need to figure out which one is which as I gave you a link to the BJB=F1 and CJB=F2 fuse panel schedule.

1999-2004 BJB CJB fuse panel layout:
Sorry I didn't realize there was a link
 
IF there's key off power in/out of fuse F2.34 the most likely cause is a bad ignition switch. The ignition switch can and does go bad.

The ignition switch can be changed by the DIY'er. Replacing the ignition switch does not require:
  • any changes to the ignition key itself.
  • reprogramming PATS.

If you are interested in getting a full copy of the Ford service manual with wiring diagrams for your car I maybe able to help. PM if interested.

EDIT: instead of posting pictures and expecting someone else to figure out, why don't you use the fuse panel diagram and post the fuse ID's? This will show us that you understand the diagrams. As well as getting us on the same game page.
 
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