I doubt I'll ever attempt anything like this as I have a fear of Linux.

But it's an interesting project and I'll certainly be watching your progress.
2 comments. First, do you have any experience with MagicJack, or at least looked into it a fair amount? I ask because we've tried to use it in 2 totally separate locations, with different 'net connections, in different states, one of which has a pretty fat pipe and very solid connection, and in both cases it has been *miserable*. Intermittent audio dropouts, beeps and clicks, dropped calls, busy signals, on and on. I wouldn't recommend it. Skype is at least less of a "closed box", and I think there are even other audio chat systems that might interface better with Linux. If it's connection to standard land lines you're after (as I suspect), your options are probably more limited, but I bet there's a VOIP provider out there that has Linux support either directly, or through 3rd party software.
Second, you mentioned eBox, so it's probably safe to assume you've looked into all the other existing Linux variants that focus on routing/firewall/gateway. But just in case, here's a reminder: look into it.

I'm fairly sure there are some good off-the-shelf solutions. Whether they will work with your hardware is another question, and whether they'll offer you the customization you want is another question still, but I reckon the latter is surely satisfied by at least one distro out there...
- Oshyan