I had alignment issues too and the trick was to loosen the connections and twist the can.
I found that because the pipes have compound angles in them, doing this causes the mufflers and the tips to move up and down and side to side. You may not even need washers. Also make sure the end flanges of your resonators are perfectly level. Get help so someone at the back can eyeball things for you.
Trust me it can be straightened out.
