I wouldn't worry about it too much. That's the deal with metal fabrication, it's very difficult to get precise repeatable results. It is close, and I'm sure it will go.
First, I would remove the left passenger peg bolt and put some loctite on it, at least blue (med), red if you think you'll not likely remove it anytime soon. Reinstall it to finger tight then backing it out 1/2 turn so it's a little loose. Then, I would have all of the other bolts slightly loose, like the same half turn out from finger tight. Next, I'd use a ratchet strap(s) to crank things over to get the holes to line up. Also, a center punch, screwdriver, whatever to use as a drift pin type device to help line up the holes to get the bolt started can be helpful. Start that bolt, first put some loctite on it too, then torque it down. Release the straps, then go around and torque down the others. Done. Good luck.