Andy,
Your RAM is still a little low for a Server 2008 Datacenter setup, but it does meet the minimum. Are you sure its entirely the Method engine taking up 100% of the resources, or are 100% of the resources being used when its running/syncing? Have you tried shutting down the Method engine and just running Quickbooks? How is the performance when you do that? I have a 3GHz P4 with 2GB of ram and it runs fine, however I'm running on Win7 Pro N. I'd try running Quickbooks, doing some minor tasks without the engine running, and check the resources. This might rule out QB as the problem.
I don't see how the engine could be using that many resources. Have been able to perform a full sync?
- Adam