I got the same error. As far as I can tell it doesn't seem to affect the server. I'm not totally sure if you can fully ignore the error but I don't think it has caused me any problems.
Yeah, the guide is somewhat vague in places. I was often confused as to what folder a particular file was supposed to go in. I used this guide:
http://www.eqemulator.net/wiki/wikka.php?wakka=Windows and even though it's older, it's easy to follow and I can vouch that it works. The only part you might not like is that it uses Minilogin instead of the EQEmuLogin. I could not get the EQEmulogin Server to work properly. Minilogin does work but it can be fickle at times.
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