This would be for a Saturday in July for an International to Domestic connection:

JL 9, ORD - NRT Landing at 15:30 in F (if it helps)
JL 297, HND - UBJ Departing HND at 18:55 (planned domestic Japan)

Transit time: 3h 25min

Both flights booked on separate tickets.

I will have checked baggage and it looks like the easiest way would be to take the 16:15 or 16:25 limousine buses, which would put me in to HND at 17:40 or 17:50 if everything is running on time.

First question, is that enough transit time or am I just asking for trouble?

The 18:55 departure is the last flight to UBJ on a Saturday.

My other alternative is to fly into FUK, which has a flights at 19:30 & 19:40 from HND and a 19:55 flight from NRT.

The biggest difference is once I land, it is 30 minutes to my ultimate destination from UBJ vs 2 hours from FUK.

If I end up having to go to FUK, I will probably take the NRT flight and save myself the trouble of transferring airports since it will only save about a half hour of time.