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I did this. You don't have to mess with pins. Just take a snapshot of the millis() or micros() counter whenever you need to register an event - incoming GPS PPS and/or RTC PPS. If you set the RTC from the GPS PPS, you can be confident that the RTC PPS will lag by only the time it took to set it (until it drifts, of course). Once you know that interval you can also compensate for it and get even closer.
I've made other sketches that compare the CPU clock or RTC time to incoming GPS PPS, using millis() as I said, and those experiments gave me all the drift and sync data I needed. It's really not complicated.