I think there is something wrong with the wiring modifications that I did for the auto to manual conversion for my car. In order to start the car I have to put the gearbox into a gear, if it is not in a gear the car won't start. This seems opposite to me, as I would have thought it would be more likely for a safety feature that the car be in neutral. Any ideas or is this normal?

Sounds like your neutral switch may have been replaced with a reverse switch.
I'm pretty sure they are the opposite. Reverse switch = Normally open, Neutral switch = normally closed.
You could just take the wires off the switch and join them so it will start at any time.

I connected mine up to my neutral switch, but the switch is buggered so it will start whether in gear or not.

You can always just bypass it and have it always closed. I don't think my (now older) new gearbox came with a neutral switch at all. I normally just check to make sure it's in neutral before I start anyway.

sounds like you have the neautral switch wired up the wrong way, mine starts only when not in gear, if in gear it acts like an auto in gear trying to be started and does nothing. As others have said you can just remove the wires from the neautral switch or swap the wires around. I prefer it to not start in gear anyway incase i or some one else driving forgets the car is in gear and saves the 'leap' foward.

Which is exactly why I am trying to figure out why it is backwards...