I am travelling right now but will download your testcase as soon as I return. In the meanwhile would you please try this earlier fix to see if it helps:
Just replace the mobi_split.py one with the version from that link.
As for fonts, I can not easily remove their sections because the older mobi html references section numbers in the mobi for images and things that may be intermixed with the fonts. I can modify the code to create sections of 0 size to replace them but I am not sure if any Kindles will have trouble with 0 sized sections. If I could prove that all fonts come after all jpegs/images then, they should be removable.
I can provide a test version of mobi-split so that you can test the version with fonts replaced with 0 sized sections. Hopefully the earlier bug fix will fix your issue with the Paperwhite as well.