There is supposed to be a gap, equal amount on both sides.
After you get done with the gap adjustment, with the bike on the center stand, rotate the rear wheel with the transmission in neutral, to see if you hear any noise from the universal joint area.
There's an small chance that the universal joint could be contacting the swing arm housing, if it is you will hear it.
I usually hold off on securing the rubber boot over the universal joint, until I set the gap on the swing arm bolts, just to visually see if there is any problem with the universal joint clearance.