After a few days of runtime, finalization of the software configurations, and letting things settle... here's what I've got.
#1 - Zacate itself is just fine for running WHS. After letting things settle and cache for a few days, the OS itself is running fairly peachy.
#2 - I'm going to laugh inside at anyone else that suggests getting a SSD for this machine. I want a file server, not a desktop gaming rig.
#3 - There does seem to be an issue with disk speed. Now before you all go saying "I told you so...", I'm still not discounting AMD's AHCI drivers for this. Something in general seems overall flaky, and I've not once had issues with WD Scorpio Blue's with speed (let's just say I know what to expect from them). I think overall speed may be better once I get a hardware controller for storage, but again, that doesn't "fix" the boot drive.
#4 - Watching server loads, etc, Zacate is more than capable for what I intend to throw at it. CPU usage more or less stays low. Occasionally it'll spike to 60-70%, but it's still fine for my purposes. There is no reason that the CPU itself shouldn't be considered powerful enough for a file server or WHS. If you want it as a general purpose server on the other hand, that's another story.
At this point I'm satisfied. If I had more time to play around and not push this thing into service, I'd play with various drive configurations, etc. But right now, it works. I'm satisfied.