I travel only w/ carry-on if I can. Just sayin"
The cutoff for checked bags is when one can no longer print the tag out at a kiosk, so time needs to be allocated to actually be in front of a kiosk by that cutoff time. Certainly can't blame OP for results - just ran into a couple of annoying (and time consuming) hurdles. Seems to me the AirTrain at EWR has hiccups during the winter more so than other times. A couple of Decembers ago, they were using buses between the rail station and the terminals because the AirTrain was kaput - that's one factor I put into my calculations now when arriving to EWR from NYC. OP took 1st train out of Penn, so outside of cab/Uber did best he could.