OK, I messed it up. I don't really want to reply to my own post - but maybe this will make it more clear to others if they get the same issue.
Been re-reading the forums for like 6 hours and I stumbeld across my answer in a post from 2008. I was pointed to the Launcer.exe now WoW.exe in each of my commands. Not sure why that affects anything, but obviously it does. I changed them all and now it appears to open correctly. I'll do some more playing with the 2nd problem tomorrow.
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