The alignment should be to the bore as it leaves the barrel vs. the outside of the barrel so putting in an indicator rod is one way to check, keep in mind that and indicator rod is going to have some slop where the sleeve is at the end of the rod, they have a taper so they stop as you put them in .. and the rod alights to the end and the point at the taper it touches the lands.
You should have clearance around the rod..
I recommend using a bore scope you your suppressor to see if any of the barrels are broken or damaged as well.
