Unfortunately, your description gives me very little to go on. I have no idea how many files you're serving up, how many mailboxes, what sort of application you are serving, what your system specs are, etc. My recommendation would be to do what you can to give Exchange 2000 its own system. If you have as many mailboxes as you have workstations, then a decently sized system with at least 512MB of RAM should work fine. Some other things you will want to do is make sure you have the latest Service Packs for both Windows 2000 and Exchange 2000 installed, and that you have all necessary and relevant updates from Windows Update and Microsoft's security site. Also, keep an eye on Microsoft's exchange site for an upcoming Exchange 2000 performance and tuning white paper that is nearing release.
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