I can see where wheel drag will affect simple thrust measurements  I can also see the problems with setup drag.  Is it fair to conclude that any thrust measurements will be on the low side due to these factors?  Do you think it would be more than perhaps 10%?

I would think that changing thrust changes from different props or fuels would still provide a reasonably  accurate difference between thrust measurements.  Something you could make a decision on. 

e.g. If a 12x6 give 6 lbs of thrust using the above method and a 13x6 gives 7 lbs of thrust on the same airplane.  I cannot imagine an error so large that the 12x6 would actually give more thrust.  Am I missing something?