Why the javascript? If you are working something for e-ink readers, they can't use it.
Fancy boxes can be displayed on some, but not all readers.
WP will generate relatively useful code, but not if you load it down with tons of styles and javascript.
You just can't control the placement of everything in e-readers as you can, and perhaps should, on paper. Tables are problematic and have trouble keeping useable size if they contain much at all.
If it is for yourself, for a particular device, you can do anything so long as it works for you. Inline styles work, but they can be a real bugbear if you decide you want to change, for example, how the names of ships or aircraft should be displayed. Italic, bold, big small, all easily done with css, where you change it one time. The way this is structured you will be editing it forever if it needs any changes.
Many readers only display shades of gray and some will be unusable as text colors.
If you have a flurry of existing documents in WordPerfect, you can save them as HTML, but you will be using regular expressions to pull out all the superfluous stuff. I didn't try plain HTML because the sample I pulled up didn't seem to need it. But that may be the best course of you if you want to avoid a lot of searching and replacing. Put in the emphasis yourself, change margins yourself in Sigil to get the effect that is possible in this limited format.
If you've got to have fixed text and spacing, then WP will easily spit out pdfs which many of the readers read. Just make the page size conform to a typical reader as they have done at feedbooks.com.
Footnotes are probably going to need to be constructed in Sigil as endnotes to each chapter to avoid jumping out of the document, which can slow things down. It is easily done in Sigil, but you will have to link to them and link back from them, since you should not assume every reader has a back button, nor that they should go back to the exact place they came from.
In short, it will not translate like you want it to translate. But then that is why Sigil exists.
You can download a epub from the MR library here and examine its stylesheet either by unzipping or opening it in Sigil. You can copy it to your hard drive and alter it to suit your needs. Then paragraph style, for instance, can be controlled by the stylesheet, after you eliminate all of the stuff following <p by regular expressions.