Wow! I don’t imagine too many sellers would go the extra mile to satisfy a buyer like yours did.
Since the previous owner did a bunch of work on it, I’m wondering if your problem could just be an adjustment. If the shift pattern plate is not adjusted properly, it may not be allowing the gear(s) to fully engage. Before you swap out the trans, try this.
Loosen, but don’t remove the two screws that hold the shift pattern plate down. You want the shift plate to be able to slide around. Shift into third gear, adjust the shift pattern plate so that it is not (or barely) touching the shift rod, then lightly snug the right shift plate screw. Then repeat the procedure for fourth gear and snug down the left screw. Then make sure you can shift into first, second and reverse, then fully tighten both shift plate screws and give it a try.