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I'm sorry, the input frequencies are maxed at 300 kHz not MHz
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Ok, that is a significantly lower frequency :)
How accurately do you need to know the phase difference? A 300kHz waveform has a period of 3.333us or ~3333ns, if you sample this at say 100MHz (10ns period), then you will have errors due to synchronizer delays, and so can probably only measure the relative phase to around 30ns accuracy, which is 30/3333*100 = 1-percent error, which may not be bad.
The alternative is to use DSP and cross-correlate the signals, or use something like the Goertzel algorithm to extract the fundamental frequency for each signal and then cross-correlate the two signals to estimate the phase-difference.
Cheers,
Dave