Thanks guys, the motor problem was a simple fix, I wired the motors to the opposite connectors, so motor one was running off of wiring for motor 2, and vice versa. I took a few hours today to work on other issues, like the track alignment, the damaged pins etc. I also got around to weathering and adding a few scale accessories to it! I have to say I'm pretty much hooked on it now that it works, this thing runs like a bear; I cant believe the torque of this brute, it'll go over anything!

EDIT: Every ten minutes of driving a few pins start to come out, is this normal? Its driving me to the point where I might just go with a weighted plastic track..