1st is the running board seal set not have the seal retainer?
38-8901 includes the running board seal & seal attaching plate.
I think the running board seal set 30-2330 on Lumbersawyer's link is just the rubber but it appears that what you found with the rocker panel also includes the running board seal and its retainer. That's good.
Your floor pan patches look decent, especially if they're 16 gauge, which is heavier than stock.
The attached picture of yours with the red line added shows where the inner-to-outer cowl piece connects to the inner cowl panel. That's going to compromise strength a bit if not fixed. I'd recommend that you replace the inner cowl, inner-to-outer cowl, and outer cowl on both sides. You have some serious rust going on.
I'd also recommend that you start a thread for all this in the DIY Gallery
HERE That'll get everything in one place on your project, rather than piecemail in various forums (you already have two threads here in Paint and Body.)
