From what I understand - you have a correct EET installation, the one that contains your logs you posted. You got remnants old old games that you clutter with that new one and - as expected - you get crap. You can have multiple game installation but you need to configure them correctly if you want to use them independently. You cannot mix them like you did.
Sorry, I know it's confusing -- no, I never have multiple installations. The second BG2 installation I mentioned was simply a file archive (a backup, really) of an old, working copy. I extracted it just to get files from a working installation, and when I did, I tested it to make sure it worked. If I install a game, I uninstall it first, and I never have multiple copies when I install.
You can do this - delete (or move to a save place outside of documents) all the folders in mydocuments that refer to Baldurs Gate - ALL.
Go to the BG2EE you have on D: verify that in engine.lua you have this
engine_name = "Baldur's Gate - Enhanced Edition Trilogy"
and start baldur.exe directly out of this D:.../BG2EE directory. Select a campaign and create a player. Check in the mydocuments that a new folder named "Baldur's Gate - Enhanced Edition Trilogy" is created.
This should solve it. You may afterwards need to open the Baldur.lua in the newly created folder if you want to activate the console and cheats for the new game, not sure about that.
Yeah Check, Check. Check. Check. I do each of these before I run BWS to make sure I have a clean system. BWS has fouled up my system somehow. I went through the process again (a couple times) with just a minimal config on BWS. Initially BG2EE works fine. After running BWS, the BG2EE game brings up BG1.
I know what to do now. It's just going to be a pain in the ass. I have to do a manual installation. And I have to be sure I get everything right. I don't see how that could corrupt a working installation.
Edit: I just found BWS-EE. I'm going to try that.