1000 users?  That's not very much :)
I've got 5.5 servers that handle more than that.

I think your plan will work fine.  You may want to consider using multiple
backend servers, but not for operational effectiveness.  More to keep from
putting your eggs in one basket so to speak.  If you have a failure on that
one server, you'll effectively take out the entire population.  Vs. having
two smaller servers where you might take out half the population.

The 200 users limit might be a reference to the CDO OWA concurrency barrier.
Some swear you can't get more than 200 simultaneous 5.5 OWA connections
going due to the limitation in the architecture.

The number of message stores is something you'll have to figure out.
Generally, if you're going to use Enterprise version of Exchange, you may
want to spread the users out over multiple stores and storage groups to take
advantage of smaller stores. This allows for faster backups and restores as
well as maintenance if needed.  In your case, you can take advantage of
single instance storage if you leave them in a single store.  However, I
think you should use a few stores (3?) so you can have smaller stores to
work with.  You won't get a benefit in the backups if you use one Storage
group so it's left to your discretion and comfort level.  I would not want
any one store larger than 100GB if I could help it.

Al