Drivetrain Transmission Help

Ok, here it is. For Valentines Day I bought my wife a 89 GT project car. She wanted something she could make her own, and the price was right for a decent car. The previous owner had pulled out the bolt on the side of the tranny and dropped the 5th/Rev arm inside thinking it was the fill port... Anyway, my brothers-in-laws and I dropped the trans and opened it up to discover it was actually a non-W/C and found a recipt in the car from the owner before the guy we got it from from a salvage yard. No biggie, we ended up going to a local transmission shop and after discussing options of rebuild vs buying a rebuilt W/C, we ended up buying a W/C.

Now to the real question. After we installed the new tranny, the shifter box sits father forward then the opening in the floor by about an inch or so. We had to notch out the opening to get bolts into the shifter, but it seems to work ok. Why did the transmission not line up correctly, was it still a wrong one? Is it going to be a problem going forward?

Any help is much appreciated.

Thanks