[Toxaris]

You would be much better of to just use the header styles in Word. It doesn't matter how it looks after conversion to the ePUB. The looks can easily enough be changed with some styling in the stylesheet. It is all about structure. An ePUB can be split into two parts, a structured part and a part that defines the layout and looks of the structured part. In your source you want the structured part as correct as possible. The layout and looks part can then easily be adapted to the target format, whatever that may be.

You road is only giving you more work now and for sure later when corrections are needed. I know of only one 'publisher' that has a automatic conversion that is not that good, and that is Smashwords. Their process is, aptly named, Meatgrinder.

Font embedding can be difficult, but usually the hardest part is the font licensing. A license for ePUB (electronic publishing) is usually more expensive than for printing. Subsetting a font may result in lower license costs, but is no way certain. Obfuscation also will not matter, it can easily enough be circumvented. If you want a low-cost solution, try using fonts that have no license costs for electronic publishing. I believe Charis is such a font, but I am not sure at all about that.