The Pro and the Sport v2 use the same main shaft. On my Pro V2 I had to loosed the bearing blocks in the frame, and squeeze the hell out of them and then my bolt would just barely go in. If you watch teh videos I had said in an early one where the auto gear was way too tight. By squeezing these together, it allowed me to use NO shims and had a perfect fit.
When you put the bearing blocks in, you want them in a way that the main gear and the collar will hold the bearings in. Meaning with the blocks installed, the top bearing will go in from the top and the bottom bearing will go in from the bottom.
You are correct that the Sport and Pro are two different bearing blocks, and it's also a totally different setup for the servos, but they use the same shaft. I do not suggest the one with the slip collar because it's not as secure as the new Pro shafts.
So loosen up the blocks and pinch them together really well. Make sure the bearings are seated all the way and try it. If you have to, and this is a last resort, use a micro round file and file the holes a little to make the blocks sit closer together. Do this a very little at a time. You can always remove material, you can't put it back. From the sounds of it, you are just a fraction of a MM from getting this. Once you have it where the main gear will go in, loosen the blocks, install the main shaft into the bearings and use some thread lock and secure the blocks. This will assure you that your bearings are lined up. Good luck.