The easiest way to check rear wheel alignment on a Dyna is by the two little "witness marks" on the rear swing arm. These two marks are just forward of the axle. One on each side of the swingarm. Measure from the mark back to the center of the axle on each side. The distance should be the same with the proper final drive belt tension.
As for the rear wheel being "centered" with the frame, the only way to check that is to take the fuel tank and rear fender off, stretch a string from the center of the steering head along the frame on back across the rear wheel. Simply looking at the way the wheel is positioned in the swingarm may be deceptive. The swingarm may not be symetrical due to the necessity to clear the final drive pulley and such. The engine alignment shouldn't have anything to do with the rear wheel alignment.
For something as serious as wheel alignment within the frame, I'd take the bike to a dealer somewhere and have them check it out. On some bikes, there is supposed to be an offset betweent he front wheel and the rear wheel. Use a piece of straight piece of square aluminum tubing to check wheel alignment.
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