I always play with TC/AP but i dont use Improved Khaak i use Revenge of The Khaak 2.0 by 7ate9 imo he's one of best scripter's/modder's on X series, but i have advice for you...dont use any Khaak mod before you start AP plots because it can cause bugs.
Also TC/AP plots are now fully functional, i didnt found any bugs, also i did use IE and it caused severe bugs, shame i really like IE, but that was 5 months ago or more so i dont know if IE got updated.
In the moment when I truly understand my enemy, understand him well enough to defeat him, then in that very moment I also love him.
-Andrew Ender Wiggin