Eddie,
When I did my alignment, I used 2, 3/4 inch nuts as standoffs from the rim. Their tolerance was close enough that it did not change my calculations, but made the process easier getting the straight edge out beyond the tire sidewalls.
Did you do the alignment with the weight on the wheels and the stress off the gear. Let me explain, when weight is put straight down onto the wheels (as in lowering from a jack) or if they roll with some side load (due to misalignment), the gear will flex and could change your calculations. One way to alleviate this is to use 2 metal plates with oil/grease between them under the tires.
Ralph