So I swapped my dead battery today for a new one and made a mess of things trying to wire it back together again. The electronics aren't a problem, its the terminal cables I'm having problems with as to where they go. I have a short one starting from the positive relay that I'm pretty sure goes to the positive terminal on the battery, then 2 more cables that I'm unsure of. Any help is appreciated!!

Tried fooling around with the wiring, now every time I connect a terminal (to what I think are the right ones) the bike tries to turn over. The keys aren't even in the ignition and the kill-switch is on, so I'm technically hot-wiring the bike. Again any help is appreciated. A HUGE help would be taking a picture of your current connections inside the battery box so I can wire mine the same.

The first area I would look at is the connection at the battery relay for the starter.
The red wire to the battery goes to one side of the relay and the connection sounds as if it is bassackwards.
You are sending battery current directly past the relay, sans use of relay at all.
The relay has ? two? fuses on the top and two locations for terminals. Switch the two hot wires and try again.
The ground wire is directly to the battery and I doubt this is a problem due to the fact that you are creating a closed circuit when it is applied.
There was no need to remove the terminals from the relay, just a battery disconnect. This is wre the problem started.
I believe that the starter relay also energizes the rest of the bike through the main fuse. You will only get a starter winding and no other electrics will function in its current( parden the pun) state of fucktupness.

Thanks Drib, I'll give it a shot tomorrow. Any other inputs are welcome, especially a picture (hard to fook that up).