If you call Edirol asking about a calibration I expect they will tell you that you have unreasonable expectations. If you want them synced, you probably want devices that sync via word clock, or digi feed. With my Alesis HD-24 and my pair of Presonus preamps (with their own A/D), I have them all hooked up via word-clock (coax and BNC's), and they sync. If you had a V3 and 2 HD-P2s, you would run SPDIF into one, and hook the word clock up on the other.
In my experience with trying to mix things from difference sources, .100s per hour drift is typical, and maybe better than average. When I was a newbie mixing UA-5 > H120 against R09, it was typically .300s per hour. Sometimes you get lucky... I've had 2 UA-5's align very closely. Just as you had 2 R-44's align closely. But it's random. Doing those kind of matrix's gets old fast.
You should be able to get a "poor man's sync" with 2 R44's. If you patch the SBD channels via SPDIF from one R44 to the other, then the downstream one should sync to the upstream one. Then you each run your own mics into the other channels, and if you wanted to align the mic sources, they would be in sync. I've wondered if an R44 could record 4 analog channels, but sync to the clock of a SPDIF input, even though it's not recording what's coming in on the input. If that's the case, they your pair of 4 channel decks become an 8 track combo, rather than a 6 track combo. I don't own an R44, and so I've never tried it, and I don't know anyone who has.