Yep, that's exactly what I had to deal with. Screw the panels in place to match up with the door pillar, then go to work on that corner till you get it to close the gap. You don't want to move the inner panel forward to meet the toeboard. I think a fair part of the issue is the shape of the floor panel. I would get that in place first (again, with sheet metal screws temporarily, if you can do that) and work both panels to close ujp the gap. Also pay attention to the angle of the toeboard as you mentioned. I had to cut and reweld my floor patch panels at the floor/toeboard bend to get the whole floor flat across the cab.
I did not get the shorty inner cowl panels from Jim Carter. I think I got them
here.
