The door check strap seals as Dan has mentioned if they are badly compressed or perished will allow water to track down inside the door post then out into the footwell.
However looking at your pictures you have pin prick holes in your inner sill section within the companion bin area as you can see water tracking down.
This in turn will drain out of the companion bins into the flutes in the floor and then will track along them eventually going under the crossmember.
Seal these up first then see what happens. Also replace the door check strap seals as well.
And just to add here the inner sills have not been replaced inside the companion bins so not full length and possibly they were the inner sill repair sections like these
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Now this in turn can also cause water leaks from within the crossmember as there is now potentially a gap in the inner sill face where it goes over the end of the crossmember. If there is any perforated metal caused by rust in this area (highly likely as this is also the area where the jacking is situated and its mounting bracket) like this picture below
