JRpass vs Air Travel

Hi!

My boyfriend and I were initially planning to get the JRPASS as we wanted to maximize our travel to Japan. The plan is Tokyo-Hakone-Nara-Osaka-Kyoto-Tokyo. I was finalizing our itinerary when I came across an advise that we can also fly back to Tokyo from Kansai. Upon checking this option and comparing the total fares for our 7day trip with a JRpass vs without a JRpass and flying with Jetstar, the latter will be 4000-5000 yen cheaper.

My concern now is the flight from KIX to NR. Jetstar leaves Kansai at 4pm and arrives in Narita at 5:30pm. How often does this airline have flight delays/cancellations? Our next flight will be international from Narita to Abu Dhabi which departs at 9:40pm. Is 4 hrs enough to accommodate any unexpected delays? Also, as we are foreigners flying domestic, will there be a hassle in the check-in process? I hope somebody can help me with this. Thanks!