You must run a ground in the same conduit as the rest of the circuit conductors.

"There will then be PVC conduit with THHN/THWN running from the Juction boxes to the Panel. "

You are likely to encounter conductor derating requirements for the large number of current carrying conductors in the home run conduits.

Is there a reason you aren't just putting subpanels in the basement and the second story? Seems a lot easier to pull 1 line than a bunch. It also would make future expansion a lot easier.

Bill - Thanks for the input. I'm not sure why the contractor didn't suggest the subpanels, but I'll ask him. They seem like a good idea, especially since we're going to have to run multiple conduits from each junction box to the panel due to the space constraints and derating.

Can't put a panel in the attic unless there are permanent stairs leading to it. there may not be enough space in the basement location to fit a panel with clearance requirements what they are.

I just met with the electrical contractor again tonight and, ionized, you are exactly right. No space in the basement with the appropriate clearances. Ditto the 2nd floor, since it a cape cod style. Guess we're going to be staying with the junction boxes.
Thanks to everyone.

Hallway wall on the second floor? The folks who wrote the NEC are less concerned about appearance than about their approach to safety.

Why not cable? Is conduit specifically required in your area?