Since the coolant was in 2 different cylinders I wouldn't put all my money on a head gasket failure, as Geordi said he has never seen 2 cylinders fail like that, apart from each other. You said water had collected in the low spot of the boost tube after the inter-cooler. Seeing water/coolant here makes me think 2 things, somehow it has leaked past the intake valves back down into to the boost tube from the cylinders, or that if you have an EGR still hooked up that it may have failed internally and is leaking/pushing coolant into the egr return gas stream, perhaps it had failed awhile ago (like you said missing coolant for some time), and on your wife's way home it failed worse and leaked a lot more coolant into the intake, maybe with the engine running it was able to still run and make it to where it was parked. I just would worry about you doing the head gasket and possibly not doing a Weeks elbow/egr delete and locking up the engine again after all that work. With the water ingestion possibly coming from the EGR it could have filled one of the cylinders just enough to break one of the rockers before it was shut off/parked, or a massive head-gasket failure happened in 2 non adjoined cylinders.
_________________ 2005 Jeep Liberty CRD, 2.8L, 4x4, bought 5/2/2015 with 120k, Timing belt/water pump, Engine mounts, Fabricated aluminum boost pipes, Auto-meter ultra lite Boost, oil press, and trans temp gauges, Straight pipe exhaust, GDE Eco Full torque Tune, Cummins in tank Lift pump, viper 1 way remote start, V6 airbox, AEM Dryflow air filter, oil catch can.
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