Yeah, none of those reference types will do you any good in a kindle MOBI anyway, with the exception of the "toc" entry and the first "text" entry (kindlegen will only use ONE reference item of the type "text". And it will use that to create the point at which to open the ebook the first time). The cover is taken care of with the meta-name "cover" and the corresponding entry in the manifest.
Just get rid of all the reference items in the guide section except:
<reference href="Text/Section0004.xhtml" title="Table Of Contents" type="toc" />
<reference href="Text/eFT_layout1.xhtml" title="Text" type="text" />
...and if eFT_layout1.xhtml isn't where you want the book to open to the very first time... change it to the file that IS where you want it to open. Such as:
<reference href="Text/eFT_FrontMatter.xhtml" title="Text" type="text" />
<reference href="Text/Section0010.xhtml" title="Text" type="text" />
or whatever you want.