> I always underline ш and write a line over т (which looks like m) to distinguish them

I used to do it as well! But I gave up on it for the same reasons I described in the article: impaired working memory.

> лишили лилии

That’s a tough one, but I think it’s possible to make it legible with careful choice of spacing to indicate the groups: the distance between the strokes within a letter should be noticeably smaller than the distance between letters.

> I also normally write д as ∂, which breaks the flow.

I also like this variant of ∂, though I eventually switched to the version with a descender. It doesn’t annoy me because it introduces only a short pen lift.