Well after letting Steam "fix" it, then adding the mods again, it seems to be okay now. I've rebooted and it's not trying to screw with anything. Hopefully this lasts.
I wish the mods would let it start without Steam.
When I bought Hearts of Iron II off of Steam it wouldn't start without Steam until I added the mods, and I can launch it by itself.
Oh well, it appears to at least be working now.
Now I'm off to go sink the Jap navy in my obsolete pig boat using broken torpedoes!
Wish me luck!