This sounds like an odd problem. if the secondary was 1" too low there is no chance at all the scope would have passed any quallity control in any factory. You may be able to wind in your 3 primary collimation screws some 10mm or so placing the mirror further up the tube to aid in your lost focus travel.
What brand is the scope? If it is a used one perhaps it had been modified as a photographic scope, thus the lack of focus travel
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