I finally got it to work!
Here are the steps I took, I hope it helps.
1. Made a nand
2. Used Scott's 10x wipe.
3. Did a fresh install of the Rom that I'm using(rezrom 3.4) including the kernel
4. Used v.1(for ics windows), it took about three times to get the timing right.
5. It said it was "rebooting to bootloader" but it went to recovery for some reason.
6. I rebooted my phone from recovery, the program found my phone and finished.
7. I had to flash the internal sd fix from the op.
8. All is good and s-off.
I hope this helps, I had been working on it for ten hours before I got it.
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