*** UPDATE ****
After inventing some new swear words, I finally got the pump out. As suspected, the splined shaft was snapped off. Luckily, the splined piece came out of the forward drive pump reasonably easy. I suctioned out about 2 gallons Hydraulic fluid from the sump hose (and lost about a quart) so I'm sure the pump never ran dry. I checked the drive pump shaft and it spins when the engine cranks so I'm pretty sure the damage was contained to the gear pump. Hopefully, restoring charge pressure will also cure the drive noise and flakiness.
I don't think the system was contaminated since the shaft broke outside of the pump. Would you guys still cut apart the filters and purge the system?? Seems like a huge pain.
I'm pretty sure I'll need to replace the whole pump but it's a shame I can't buy just the shaft and a rebuild kit as the pumps internals seemed strong.