I thought I would do a follow up to my original post.
To recap - I bought a ticket SFO-JFK-LHR UA956 and didn't understand that even though I was landing and changing planes that I would only be credited with the miles of a direct flight.
I tried to sever the flights before I flew, and 3 calls to UA Reservations yeilded nothing.
I then attempted to stand by for an earlier flight. Unfortunately the day I flew out of SFO, the PremEx line was stood still - caused by some guy who needed 45 minutes to do something special at the check in desk, leaving only 1 agent to help all the *Gold passengers. The 1K line was almost as long, and perhaps as a result of all the EQM bonuses, the 2P line ended up being the fastest. I missed the standby window by 5 minutes, but the GA though that had I been able to stand by that I would have been credited correctly.
I did manage to upgrade, but unfortunately I could not find anyone (either in SFO or JFK) who was willing to issue me a new 2nd boarding card that didn't say "Reboarding" on it.
After I got home, I tried calling M+ several times, but they would absolutely not budge - even after I explained that I needed the miles for 1K and would have to book needlessly complicated flights the rest of the year. So I'm now needlessly booked on 2 connecting flights (rather than a direct) and on 2 more nearly sold out airplanes (vs. 2 nearly empty planes) which will waste 6 hours of my time and generate no additional revenue to UA just because the M+ people are so inflexible (to maintain the integrity of the M+ program).
But ---- the funny thing is that just today, I logged into M+ and found 10,000 miles extra in my account, posted as bonus miles for the USA-LHR promo. Had they severed the flights, I would have only recieved the JFK-LHR segments as bonus miles, but since they were so pigheaded, I ended up with about 3000 more miles in the end anyway.
Go figure.
Lesson learned: if you want the EQM, make sure your flights are booked as 2 segments from the start.