I live over in Newport News, so I feel your pain. Long, long ago I gave up trying to connect out of Hampton Roads to head to Florida (I take the train that way about 4-5 times per year) and just got used to driving/riding to RVR.
The connecting times from the evening train from NPN isn't horrible, but it's still a 2:30-ish layover at a suburban station without a whole lot obviously around it. The other connection pairs are, however, somewhat toxic (Star-to-Regional is something like five hours, Meteor-to-Regional is close to the same, and Regional-to-Star is about six hours). One thing I've been trying to nudge for is a bit more thruway connectivity, such as a midday bus that would at least knock some of those waits down to <2:00. As it stands, practically speaking I often can't even take the train to Richmond for a meeting from here, something which makes me pull my hair out since it seems to be a "natural" city pair (what with service into RVM and all).
For good or ill I expect the second NFK train to either be a return to the 0500-ish departure NFK used to have or for NFK to "steal" the morning train out of NPN and for NPN to get one of the early-ish departures. Basically you've got NB Regional departures from RVR at 0600, 0700, 0800, 1104, and 1900. The 1900 train probably isn't moving (I wouldn't be deeply stunned if that happened but I'd happily take a $5 bet against it for now) which means you're shuffling the others around...and 0600 is a problem because that puts you coming out of NFK at about 0400 (which is a stretch even in a military town). So now you're allocating 0700, 0800, and 1104 between NPN and NFK.
TBH your best bet would be the third train, which if I read some of the nuances in the various plans would probably be set up to connect with another train at RVR (for the simple fact that allocating anything to the 0600 train is a problem and you've now got six brides for seven brothers, so to speak).