@doubleshuffle,
I think your problem with 'lost text-aligns' is because the kepub renderer enforces overriding CSS for <div> and <p> elements. By default it has the following sledgehammer applied:
Code:
div, p { text-align: %1 !important; }
where %1 is your Justification setting in the Kobo's Aa menu screen.
If you're already using the Kobo Patcher for other tweaks you should try enabling the patch labeled
Code:
patch_name = `Un-Force user text-align in div,p tags in KePubs`
The patch changes the override to
Code:
body { text-align: %1 !important; }
which matches the override for standard epubs.