While I was snooping around the web I'm sure I read that another model Honda that shares the E07 motor uses the same auto box as the D series civics, would that not mean that manual D series boxes would fit too? I know the ratios are off but there might be a way around that yes?

I've been investigating engine swaps also and there are really no options better then whats in there already. All the new Honda motors need to be mounted the other way round which does't feng shui with the fuel tank and the engine bay is asymetrical to accommodate it. Plus the E07 is slanted giving correct weight distribution. Your never going to maintain that with a different motor.