David Blain wrote:

> Dallas DS1307 Serial Real Time Clock I2C

  Do you really need this?  The central site could poll the peripherals
each second, sending the time in the poll.  If you wanted, an "alive"
LED could pulse each poll.

> 1) Should I use one pair for both supply and return or 2 separate
> pairs one for supply and one for return? (The same pair seems like a
> bad Idea, but I don't quite know why)

  One pair should do.  The ground return resistance/ drop won't matter
with RS-485.

> 2) Should I put a voltage regulator (7805) at each thermostat

  Good idea.

> and have the supply be unregulated

  Supply would still be modestly regulated.

> Would the heat from the 7805 affect the Temperature reading?

  Yes!  The penalty for local regulation is that you double the local
heat (assuming 10V supply).  Local heat generation is a problem you
have given yourself by using a Scenix clocked at 50MHz!  You need to
locate the DS1261 well away from and *BELOW* the regulator *and the
Scenix*!  Note I say *below*.  Convection from the heat-producing
devices could actually improve your sensing accuracy if vents are top
and bottom only.
--
  Cheers,
        Paul B.