I can't help you with the second issue you have with your InDesign fixed ePub without seeing the files you're working with, but I can address the first for you.
You cannot embed fonts in a fixed ePub that you do not have. Your fonts from Typekit are provided through cloud access to Adobe servers. Essentially they're not held on your machine; they're held with cloud access to Adobe. While there are technical quibbles with the statement in my last sentence, it's effectively correct and you cannot embed fonts you don't have on your system.
You need to use resident fonts on your system to embed them in an ePub. Sorry I don't have a better answer for you, but that's the way it is.
Randy, that is incorrect. The fonts are not only installed (but hidden) on your machine, they are are indeed embeddable in FXL EPUB as well as PDF.
As for ADE, make sure you have the most up to date version. I think the current version is 4.5.3 but it is not the greatest EPUB reader. iBooks is superior as is Readium for Chrome.
Thank you for your information. I did not realize that Typekit fonts were embeddable.
I didn't really want to get into the hidden part though ...
Thanks for setting me straight.
Thanks for for your replies. I did know that typekit embeds - since it comes up on the ipad nicely. Just not sure what the hell is going on with ADE.