Well, it's been awhile. I've not posted, but have been busy.
First of all, I wasn't originally intending to write a install guide. The original project (and still the primary objective) is an installation troubleshooting reference. Thus the reason it's a text file. It's mostly usable at this point, and can be searched as easily by machine as by man. The ability to do keyword searches on mod components (and look for issues) is helping more than you know.
I've got a lot more work to do on the text file, but have had to suspend it for now. The issue is that I have yet to be able to get a working installation following the PDF.
There are a LOT of problems with the original PDF folks. Being a Linux user, I've always done manual installations and thus already knew that. It was bad enough back in the day, but is damning now.
Anyhow, I've decided to post some of what I've learned in the event it helps anyone else that's trying to do a manual install for the original game (and likely the GOG version as well).
1) You're going to have issues with BGT. The PDF recommends using an earlier version, as the changes the more recent ones implement to the music break a LOT of older mods (starting with Check the Bodies). More worryingly they also disrupt DLTCEP (which can't find the songlist). There may be a work around for the DLTCEP issue, but to correct the errors with the rest simply don't install the music until towards the end of your install.
2) You'll need to decide pretty early on if you're going to install either BP or SCS as your AI. I don't recommend using both ... too many conflicts possible. BP is better for people who don't have super powerful computers (SCS can take upwards of four hours to just install). Problems happen if you're looking to install Ascension. The new version has major issues with BP. It also breaks a lot of older mods, which either won't install at all because of it or won't install Ascension specific stuff with it. You can install the original, but if you do you'll also need to install BP's version afterwards to get other (older) mods to work right. The older mods won't work with the new Ascension (and basically require BP), so you'll need to make up your mind about that off the bat.
3) Shadows over Soubar (sos) will write nonsense to your setup-gui file on original bg. This is bad. To make matters worse, BGT requires a (working) setup-gui.tp2, which at it's point in the install can only be provided by either SOS or The Darkest Day (TDD). BGT complains about TDD however (WARNING: cannot find block matching [bgt/compat/tdd/replace/rar0300.baf]). The solution I've found is to install TDD, move the setup-gui.tp2 to tdd/ ,install SOS, delete the (bad) setup-gui.tp2 it places, copy back the protected copy from TDD and proceed with installing BGT. Things will now work correctly.
4) On the subject of GUI mods, do NOT install BP's GUI additions and do NOT install the same from 1PP. 1PP in particular will destroy your setup-gui.tp2 file (and weidu will accuse you of using msword to edit it).
5) Turnabout will install correctly with the original Ascension IF you've also installed BP's version (won't install otherwise). Everything else seems to be ok for now.
6) The Paladins of Faerun mod apparently conflicts with the Ding0's tweak component "NPC's & Summons set off traps" (ERROR: [PF0152.ARE] -> [override/PF0152.ARE] Patching Failed (COPY) (Failure("resource [GNT2004.bcs] not found for 'COPY'")) D0TWEAK. One or the other folks.
And a million other things I'm not thinking about right now. The project is ongoing, and will post back later once I've resolved a few more issues 