Plumbing – should I rework this 3/4“ main water line into 1/2” branch circuits

That looks perfectly suitable. One additional thing you should be aware of, though - if your existing plumbing contains any yellow brass fittings, they really need to come out because of a chemical quirk of PEX; the zinc gets leached out of yellow brass, leaving behind only soft copper, and the fittings may either leak or plug solid. You can use RED brass, just not YELLOW brass.

The manifold should be one size larger than the pipe supplying it.

If there's any question at all about grounding, a solid ground rod can be driven... with the result of giving you a better ground than you ever had by grounding through copper pipe.

Like copper, PEX requires a 1/4" drop per foot (never install it level or wavy), and requires a drain at every low point so the house can be winterized if necessary.

Is there any particular reason for going with PEX instead of tending to leaky fittings as you find them? I suspect that those fittings were always leaky because they were never sweated together correctly in the first place. I ask this question because replumbing the entire house in PEX is really a large, expensive job... while replacing (or resweating) one fitting at a time is relatively cheap.

I doubt you need the second 90 (#3) - PEX is bendable at large radius, and if you work with that, you avoid fittings that may have freeze damage (PEX itself does not mind freezing.)

If you think of it as if it was rigid pipe, you end up with a lot of fittings. If you work with its strengths, you can avoid many of those fittings, but you don't get tidy pipe-like runs.

I would be concerned with complete drainage ("slightly angled down while running under floor joists" may work for properly hung rigid pipe - pex is not rigid pipe.)