Here are a couple of other suggestions:
1. Do you really need to filter at all? If the goal is to measure the delay, then I would think the fundamental frequency should do. Instead of trying to clean up the second signal, you could extract the fundamental frequency from both signals and compare the single tone phase (using Extract Single Tone Information on both signals). The extraction VI is not a filter, but can be easily used to return the extracted signal (using the "export signals" control and the "exported signals" output cluster). In this way you have the option of interpreting the measured phase or in working with the extracted single-frequency signal.
2. If you must filter and phase delay is an issue (as in your case), you should always consider linear phase FIR filtering, which delays all frequencies equally. The delay introduced, in samples, is (M-1)/2, where M is the filter size (number of coefficients or "taps"). For M odd, the delay is a whole number of samples and may be easier to handle. As you are working with Waveforms, you can use the Digital FIR Filter VI located in the Analyze >> Waveform Conditioning palette.