The latest version is available for download:
NeJ3 v7.1
Installation order is very strict:
SoA-ToB + ToB official patch (v26498) + Vlad's Compilation v2.1 + NeJ3 v7.1
It can be installed on top of BGT as well, and it is fully compatible with BGT including the smooth transfer of your NPCs from BG1 to BG2 and story-line continuation.
The installation of the BGT version is as follows:
BGT v1.18 + Vlad's Compilation v2.1 + NeJ3 v7.1
Possible installations:
Alternative 1:
SoA-ToB GOG + Vlad's Compilation v2.1 + NeJ3 v7.1
Alternative 2:
SoA-ToB + ToB official patch (v26498) + BGT + Vlad's Compilation v2.1 + NeJ3 v7.1
Alternative 3:
SoA-ToB + ToB official patch (v26498) + BGT + Vlad's Compilation v2.1 + NeJ3 v7.1 + BG1-songs
BG1-songs restores the original BG1 area songs and can be uninstalled when you start the BG2 part of the game.
There are a lot of things to add as hints and the original walkthrough should be rewritten. The third part starts in Underdark via fire elemental portal. All the NPCs quests are optional but have timers. It is highly recommended to do the major quests in Athkatla to find all new NPCs and complete their quests. The BG1 locations are available through a new map with modified locations. This map will become the map of BGT if it is installed.
There is a large number of powerful items which sometimes can be further upgraded by Cromwell or Cespenar, so don't throw the important components from your inventory and visit Cromwell sometimes if you feel you can enhance an item. Cromwell will arrive to Brynnlaw, so you'll have an option to forge some of your items there.
The third path is available by opposing Gaelan and rejecting Bodhi's offer as well. It is advisable to complete all the thieves related quests including the thief guild quests before you confront Gaelan for his key. After that you'll be constantly attacked by thieves looking for you in Athkatla. Prepare for tough fights. The same problem will be after destruction of the slaver's base in Slums. Slavers won't leave it unpunished.
Anyway, if you have questions or require hints, please don't hesitate to ask me here.
Credits for new area graphics are to Yura Popov (aka Gorion).
Good luck!