I think the java apps just need to be reinstalled, probably corrupted with all the changes. And just have to replace the firewall rules (ugh). but it seems as though most things are running correctly now.
I see find, as well as many other commands that weren't working in cmd, but its in c:\windows\system32. d: is simply the storage drive. no windows folder
I have %systemroot%\system32 in there, which I thought should default to c:\windows\system32. I copied it and pasted it to notepad, and could paste it here.