None of the other ideas (bad mic cable, bad mic, bad SD card) fit the symptoms of the pops being common-mode but no audio loss during the pops. Do the test I did: invert the polarity of one channel and then sum the two channels and listen. You'll hear only L-R sound -- the pops will be canceled out entirely as well as everything else in the center. (This is how the karaoke "vocal remover" trick works -- common-mode signals are nulled out). Whatever is causing the problem is common to both channels but isn't a bad connection or you'd lose audio, too. This has the earmarks of a voltage glitch being injected into the signal.
"The crazy part is that the first 2 hours of the show had no issues then these pops showed up for about 40 minutes or so, then the recording is fine again."
Not at all crazy. Resistors and other parts can go noisy or intermittent depending on the phase of the moon and how they feel about things. You ever take a car to the mechanic only to find that it has stopped making that funny noise?
Send the builder the track and suggest they try the out-of-"phase" summing trick I did.