Just a background, since we had leak in past, we had to replace the Plywood
as well, and that meant opening up sidings and replacing tyvek, insulation
etc. My concern was, did we ensure that Sidings/Tyvek installation was done
properly. It rained pretty heavily three days back. Thereby just checking
and getting opinion based on what I saw one day after installation of
wonderboard (and it rained the night I installed the wonderboard)


You certainly need to make sure that the leak is
stopped, one way or another, but the stain could
have come from staining in the drywall, due to
the original leak. If you paint over the joint you can
just use some stain sealer paint (after primer) to
deal with that.

I don't have any great ideas about how to confirm
that the leak is fixed, other than to open up the
wall and wait for another rain. Or check on the outside.
You should be able to see whether the siding is done
properly. The Tyvek is a wind barrier. If it's stopping
water then you'll have problems soon. Water shouldn't
be getting that far.
I suppose you could hose down the side of the house
and see if the wall inside gets wet, but that shouldn't
be necessary.