If you want your feathers to look like an X and not a plus sign need to set the jig for 75x105, not 90-90. There's an adjustment for that in the nob that holds the nock.
Shouldn't be any problem having the nock line up with the grain of the arrow. The nock goes on first, then it's put in the jig. Just line up the nock correctly when you glue it on
By too big, do you mean the throat of the nock, resulting in a little play when it's in the nock receiver, or that the outside of the nock is too big to fit into the receiver. I've never found the latter to be the case with any nock. A little "play" in the nock on the receiver is normal. Just push the arrow down on the nock receiver to reseat it after each partial rotation
You could friction fit a a nock with a smaller throat on the shaft to do the fletching, then replace it with your larger nocks. However, there's a good chance the friction fit nock could slip while you're fletching, and you might not get all of the replacement nocks on consistently. I'd opt for nocks with smaller throats. They're inexpensive. But, as I've said, a little play is normal. Probably not something you need to worry about.