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Try using SharpCap Pro for your polar alignment routine. I am not sure if it can 'talk' to a DSLR (I use it with my guide camera for PA) but if it can, you may find it simplifies the process for you. It does not require you to be able to see any stars through the polar scope (although the camera must be able to detect them), and in fact it doesn't require the use of the polar scope at all. Run the alignment routine through your DSLR/lens combo (assuming SC can communicate with Canon's) and then close it and switch to your preferred acquisition software.
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