If you have VA status I would fly DL as the US partner, not VX. VX is good in business, but not good in economy, and VA elite doesn't get you much else.
$5600 is a pretty good (or at least standard) price. BOS for some reason tends to have more expensive flights than other US cities (it is prob the largest US city that is not an airline hub - I used to live there). If JetBlue do the route their is competition and lower price, but not for most routes.
Our little one (Miss 2) has done ~50 flights so far, inc ~8 long haul and ~12 domestic US. We found the hub and spoke model in the US (i.e. LAX-MSP/ATL-BOS v LAX-BOS) was often better. Also as a general rule we find that flights between 4-6hours bring the 'witching time' (i.e. anything under 4 is okay, as is anything over 6, but between then and it's on! The prep for landing/take-off is disruptive but 6hrs or more often results in napping and more free time to walk the aisle etc and just a more relaxed experience over all). As the planes used for US domestic flights aren't the same as the international birds, and she generally responded better to having a run around between shorter hops. Have found that They also tend to be cheaper.
I also find half the time on the DL site I get a Trans-Pacific flight with a VA code anyway (and find VA often registers a VA operated flight as VA rather than DL code anyway, even with a DL code).