1) LL Intensity is the brightness of the Landing Lights, and Taxi  Lights. If you feel they are too bright, change it from Regular to Low.

2) If they are made using the default flight planner, the defauilt location, Documents\Prepar3D Files, is fine. The .RT routes are saved in the P3Dv4\Captain_Sim\navigation\routes folder.

3) *It uses Captain Sims .RT format (but it's newer than that used on the older 757 v4.6, and 767 v1.5), and the default P3Dv4 .PLN format.

4) It works on the GE90B models for me. Installation problem?

5) Press the F&P icon on the Simicon Panel (Shift+2), and you can set the fuel, passenger, and cargo for the current model loaed into P3Dv4.

6) Go to the 777 II SimOps page, and download the manual.

7) Installation problem? Do other 2D panels open (Shift+3/4/5/6/7/8)?

* PFPX saves in the older .RT, so saved flight plans from it wont work for the 777 II, unless you save them as a default P3Dv4 .PLN in Documents\Prepar3D Files (same applies to flightplans made with any 3rd patry software).

The general thing is that the 777 II might not be installed correctly (AV interference), as in the trouble with #4, and #7.
Also, it's best to run the ACE as an adminstrator, so that it has the rights to make any changes.