1) Is there any reason not to set the window sill right on top of the
mudsill? I'm aware of the need for any wood to be 6" above grade,
of the need to clear any anchor bolts, and the need to level the
sill, but are there any other reasons?

Not that *I* know of, anyway. You want to keep water
and bugs away.


2) Where the floor joists are parallel to the cripple wall, can the
window go all the way up to the top plate of the cripple wall? It
seems that when the floor joists are perpendicular to the wall, a
header below the top plate is required to spread the floor joist
load. But otherwise, if the rim joist is larger than the required
header for the opening, can I rely on the rim joist to spread the
load from the wall above?


Yes, you should be able to go all the way up, but no, you shouldn't
depend on the rim-joist by itself. You can double or triple it,
depending on how big a span you're talking about, so that you've got
a good hefty beam across the top. This doesn't sacrifice headroom,
though it may interfere with wireing and/or piping against the
rim-board.