I can't think of anything else off the top of my head that might slow you down moving your site. I know it is kind of a pain to check all your file-names with your links, but I do believe that Linux makes for a much better server than does M$. I've used both, administered both, and I'll have to say there was MUCH less frustration with the Linux server. Linux is much more secure, and for an example I run a Linux firewall on my home network which has run non-stop for the past 2 years without a single crash. Try that with Windows!
Sorry for the hassle you're facing, but it will well be worth it, as you have already seen by the response to your question here in the forum.....happy de-casing!