Thank you for the reply. All methods in fmpq_poly_linkage.pxi are now covered, and I've uploaded a new patch to trac ticket 4000. The methods all just refer to the appropriate method in FLINT, except for modular exponentiation. I am currently struggling to make SAGE use this new implementation as the default, but once this problem is solved (which I don't yet know how to do...), I should be able to add proper documentation and compare speeds.
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