You shouldn't just shut down an Exchange server, as Exchange will expect the server to still be there. If you want to remove the server then you need to remove it correctly, using add/remove programs after following the Microsoft guide.
http://technet.microsoft.com/en-us/library/bb288905.aspxI haven't had to wait weeks for everything to replicate across, a few days at most, depending on the content size. You must replicate the system folders otherwise your clients will not function correctly.
Simon.