I just picked up a 98 gsx and the alternator won't charge (Brand new alternator) and non of the electrical works except the taillights and blinkers. Runs and drives fine. Fuse box was relocated to the glove box. Does anyone know if I'm missing any fuses or what the wire with the inline fuse on it should go to? Or any suggestions on what to check?

Hard to tell. But the wire with the fuse In line should go to the battery or to the alternator.

At the fuse box one of the first two fuses should be 100amp (where the wire with the fuse in line comes from) , that fuse is the alternator fuse,.
Check continuity from one side of the fuse to the battery and from the other side of the fuse to the alternator.

The big wire that comes from the alternator goes to the 100amp fuse and on the other side of the fuse goes to the battery, see if they both are connected.

The 100a fuse was blown. Replaced it and the alternator worked plus the windows, sunroof, and CD player. Some one on Facebook thats done a few fuse relocations said the wires were hooked up wrong and that the fuse would blow again. So I hooked it up how he said but the alternator wasn't working again but the windows and CD player still worked. Fuse still good

This is how it was hooked up

This is how he said to hook it up

He says the single wore should be for the alternator

I'd save myself A TON of headache and just pick up an un-hacked harness. Its impossible for us to help/fix your problem to be completely honest. So many things could be messed up.

2^^ if he didn’t fix what he said it was wrong when he did the wire tuck, then that says a lot of how the job was done.

Your best bet will be to replace the harness, unless you want to remove the harness and go through every single wire to make sure it goes to its corresponding line.