I have no idea about the page numbering thing.
Regarding the cover being missing... I assume the cover is properly set in the OPF? (Check with the Set Semantics tool, or use Polish books to forcibly add the cover if necessary.)
I only have a Kindle Touch, but I have heard here on MR that newer Kindles have issues displaying the covers for Personal Documents, or covers of certain sizes.
One thing that has worked for some people (???) is to use the Quality Check plugin to
Check Mobi ==> Check missing ASIN identifier
select all results
Fix ==> Fix ASIN for Kindle Fire.
For some reason, newer devices don't like files without an ASIN.
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