Haunted 2004 Ford Freestar SE Wiring

[my1bike]

I put in the new battery and changed three burned fuses in the outer fuse box. First the key remote died and then the car will start but will not catch ANY gears. Also nothing is working (power windows,locks, lights,ac,stereo etc). I called in an electrician who checked & claimed that all the fuses are fine and the problem COULD be in "general electronic module" ? we don't know. anyways, the guy put in an extra wire connection to join 5 AMP fuse in the inner fuse box to the brake paddel switch. (fuse is the most right and lowest in the inside fuse box close to brake paddel). So now whats going on is that I can drive the car but nothing inside functions/stereo/ac/lights will work unless I press the brake paddle. Remote alarm is still not doing anything.I have tried to reprogram it least 10 times exactly as given in manual.
CAN SOMEONE SUGGEST ME WHATS GOING ON HERE AND WHAT ARE LIKELY POSSIBILITIES/SOLUTIONS/WAYS TO FIGURE OUT ??

[woodstockfreestar]

I hope this helps a little - there is a computer box under the floor on the passenger side of the van that was causing some electrical problems right after we got the van and the warranty ended up paying for a replacement because operating certain things like windows or headlights would cause the van to die and then no electrical to anything for about 10 minutes after it happened each time. I don't remember what the box was called, but I'll look on my reciept when I get home. The mechanic told me water gets in these through a design flaw on the van someone. They fixed it though and its been good ever since.