Alright, let me give you some history so we can get everything straight.
I have a 03 turbo s2000 running AEM EMS v2. I was having a battery charging problem so I upgraded a few things in hopes it would fix the problem. I replaced my alternator with a 200AMP high output alternator since the OEM unit was dying. I replaced the 2GA battery relocation wire with 0GA wire. I also bought a new battery.

Going down the road, I was getting into it. When the car was in high load, around 9000RPM, everything shut off and the car wouldn’t start. Nothing happened. It acted as if my battery wasn’t even connected.
I started checking the fuses. Looked at the fuse box under the hood and found out that the 100AMP and 40AMP fuse blew. I replaced both of those but it didn’t fix the problem.
I checked the under dash fuse box and found that the “POWER WINDOW-DR”, the fuse that controls the alternator, and one other fuse was blown. (I will confirm these fuses later). And they instantly keep blowing when I replace them.

When I connect the battery to the car, the truck will automatically unlock, the car has the ability to turn over WITHOUT a key, and the dash backlight is on, but nothing else with pop on. I cannot hear the fuel pump kick on, head lights wont work, etc.

Does this sound like a bad relay? A wire improperly grounded?

I went through my battery relocation wires and those are fine. I also went through my fuse box relocation and that’s fine too. My buddy suggested that the high out put alternator probably threw too much juice into the system and melted wires together which is causing a short. Is this possible?

 

How long has it been since the relocation? What did you relocate? fuse box, battery, and eps? Sorry I'm a little slow.

I would disconnect the battery, go through all your fuses change where necessary, reinstall old alternator then see if you get a result change. The alternator feeds the main under hood fuse box then it distributes it. If it's blowing 100 amp in fuse then my guess is that the new alternator is not functioning properly.

 

Yes, i relocated the under hood fuse box, the battery, and EPS unit.

I just ordered a engine bay harness and under hood fuse box with all relays, fuses, etc. Im going to replace both of those and see if it fixes the problem. This will force me to go through the harness and find the problem.