Re: measuring AC voltage
you could use a differential probe that allows direct, earth free measurement on power lines.
the question is in what you are interested.
Because you mention exessive phase shift you are probably interested in the zero crossing point of the mains voltage. This can be measured with a opto coupler.
If your transformer is very small (<5VA) then you have a lot of stray inductivity and thus results in a phase shift. May be you should put a load resistance on the secondary.
hope it helps
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