Used this guide today, with filling in of some blanks from the various other TTW/F&L/CPD guides - result is what appears to be a fully functional game on (nearly) the first try. There were a few random minor issues, and I'll try to go back through and write those up for you but most weren't anything game-breaking.
The only issue I encountered, and this is just newbieness talking, is that at one point it was necessary to disable 'Have MO manage archives' (to run LODGen, maybe?). After whatever step that was, I never turned it back on. Attempting to load the game at the end lead to sheer brokenness - the title screen became my game cursor, for example :) Once I turned that back on and rechecked everything - so far it seems flawless (granted, I'm not even out of the vault yet, but menus/HUD/graphics/mods all seem to be doing what they should be doing).
I did skip over a number of things, such as major quest packs (like I'll ever finish both games as it is...), MMM, and WMX - wasn't going for a super long and/or super hard game (and I was getting very tired and the extra steps for some of those was getting beyond my patience). It was very easy to determine which TTW compatability patches to swap in so no harm thus far in leaving them out.
Long story short, excellent guide and seems pretty complete as-is.