With that little, it's very possible that you can run for a while w/o issue. I doubt it's just casting. Double check the diff cover to see that the pin isn't digging into it.

Reprogramming or swapping the gears, as Greg said is pretty straight forward. I would also change the output shaft and diff. (Split the diff off the output shaft and make sure the shaft comes out the driverside of the trans), also remember the o-ring on the input shaft or you will destroy it.