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From what I know about the forest prep and domain prep it shouldn't hurt. When you run setup, it will actually run these two prep options when neccessary. The reason that Exchange has you run them seperate from install, is they can take quite a while to complete.

In Outlook you can have an exchange account and a POP3 account in the same profile. The simplest way to get what you are describing is setup a mailbox for each of your users in Exchange, then when configuring their e-mail on Outlook add the exchange account and change their delivery location...

silly question: Do you have the smtp virtual server running on the new Exchange server?

I am assuming that no one, whether inside or outside can access owa through owa.domain.com. If so, then you need to go into IIS and then into the default website properties, then on the IP address field, click the Advanced button. You need to add owa.domain.com here and the appropriate port...

I'm not sure that you wouldn't have this same problem even if you were to have two different names and were able to add this other server to this domain. With Exchange 2000, you can only have one Exchange organization per forest. It sounds like you had two Exchange orgs on two different forests.

This is setup by default. The address is http://localhost/exchange. if you want to access a mailbox that isn't your personal mailbox, then it is http://localhost/exchange/{mailboxname}