Pay attention to the Firewire Card - using one that is proven is worth the effort.
Watch for other system hungry software, especially if you bought a consumer level systems with the usual boatload of trial-ware, diagnostic-ware (Dell's center is really annoying when it wants to update) and some real-time antivirus stuff can cause issues.
Read the manuals and notes. Small amount of time there saves much later.
Make backups before significant upgrades.
Screen-shots and notes of settings can be useful if you ever want to do a clean rebuild.
Oh, backup everything. That hard drive likely will go a long ways, but not forever.
And most of all, remember that other hams have it all working - and working well - so ask if you get stumped or it doesn't work the way you want it to.
With Varying Frequency - http://k9zw.wordpress.com