I just went through the whole process on my own. I set up a business (商業), not a company, however. (I'm still not certain exactly what the differences are, but for my business, either would have been fine, with no difference in my business practice or taxation.)
It's fairly straightforward, but there is little to no information out there on how to get it done--not for free at least. It took me about two months in total, and less than NT$4,000 in costs (not counting my "office," which I'm paying NT$2,625/mo. for in Taipei City).
If anyone has questions about the process, feel free to PM me.