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Shims are probably the best option - so what you have done is good so long as its not going to slip out
Bearing in mind that you might be inducing some flexure into the OTAs themselves - if they are pairs of rings.
Is there any option to rotate the OTAs a little ? - you might just find that variations in the optical alignment and the physical tubes etc is enough to get you what you need, or even swapping OTAs from left to right might provide a positive correction - but it might do the opposite too !
Otherwise loosening off the screws and realignining while slightly loose and then retightening may allow you a small amount of wiggle room on both scopes.
Failing that, your final drilling option is possibly all thats left.
How accurately and repeatably are your cameras attaching ?
The cameras themselves may or may not have their chips centred on the optical or physical centres of your systems.
Is there any movement in the focussing systems ?
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