Loves me some KLR.
It is in fact a JC Whitney top box. I had one just like it on mine.
The only thing I'll mention on your list of "to do" mods is the stator. I've heard people having nothing but problems with the big stator for these. IMO, it's better to make due with the little stock unit than to have a bigger one that doesn't work at all. Especially in the middle of nowhere. Of course that means no heated gear, but at least the bike will run.
I don't have those problems with my little WR now that I've upgraded from the KLR. The WR comes with a 350 watt alternator