Phase difference circuit - Bias problem
1) Use an op amp to generate a pseudo-ground at 2.5 volts.

2) AC-couple your inputs, and reference the inputs to the pseudo-ground.

3) Reference output filter to pseudo-ground,

4) Add another comparator (not an LT1720) to level shift the XOR gate output to pseudo-ground. Alternatively, if you're not that interested in accuracy, level shift by providing a voltage divider from the XOR to +5, with equal value resistors. A fine trim pot at the middle of the divider is probably a good idea.

5) Replace Q1 with an analog gate such a CD4066.

6) Reference your output meter to pseudo-ground, not ground.