Agreed on starting with those upper openings as you decide how much of the total opening you can safely block.
As a rule, there's more advantage from blocking upper openings than an equivalent sized lower one.
As for the door bumper strips, their negative impact on aero would be really, really small (far too small to detect in testing, I'd guess). So unless you're going hardcore and truly don't care about appearance (nothing wrong with that!), I'd leave them on.
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