He uses a Mac, so pretty much all of his instructions would apply to you. His instructions assume you know nothing about html, but if you do, then you can skip some of the primer. I found a great site from Guido Henkel that takes you step-by-step through this process, and it gives you much more control over your final format. I convert my Word document to an html file (web simple), and then I do some formatting in the html file. I don't use Mac, but this process should work just as well on a Mac as it does on a PC. mobi file, it is possible that something got left behind in the conversion process and that is messing up KindleGen.
Even though you are converting that to a. Your problems are probably coming about as a result of you converting to ePub, especially since the Kindle doesn't read that format.
KDP usually does a pretty good job at converting Word documents, as long as you didn't get too carried away using different styles. Your best bet in uploading to KDP would be to leave your file in Word format and upload that.