My experience using MfE with a corporate Exchange 2003 server has been almost identical to yours. I have seen all of the symptoms that you mentioned and mfefolders helped a lot in improving the speed and reliability of the Exchange email sync on my N900.

Because MfE is quite new and Exchange 2003 was first supported in the latest firmware version, I anticipate significant progress when PR 1.2 arrives. There are already quite a few bugs open against MfE so I have tried not to add to the noise yet, but I have been collecting syslog and I have run the activesync and calendar traces at times to get ready to report any remaining issues after the PR1.2 upgrade.

If you follow Andre's link and install syslog, don't forget to monitor the log size so you don't fill up the root filesystem. The activesync logging is substantial, and the calendar logging is even more so I expect that you would want to enable them for a single synchronization session in most cases.

Good luck!