Vertical adjustment of the canopy frame can be done by adding spacers where the rollers insert into the canopy frame tubing. The spacers are made from tubing that matches the canopy tubing OD and ID. I made mine from aluminum.
I can’t remember if this was per Vans instructions or? Mine are about 3/32 thick.
The only shimming that the roll bar needs is to allow it to sit flat on the deck but I suppose shimming it would accomplish the same thing for this purpose if you have already drilled your frame for the rollers.
Be aware that you don’t necessarily want the roll bar and canopy frame to match up. You want the windscreen and the canopy to be in alignment so your fairing works. The windscreen lays on top of the roll bar and extends beyond the roll bar center sloping up slightly.
I am not sure what sequence Vans may have in the instructions but I installed the roll bar flat on the deck, installed the windscreen, then made the canopy work.
It’s good you are looking at how all the parts meet together before just treading onward. The early kits make you think and there is usually more than one solution to any problem.