Hi,
FPSC-2-AGK is designed to be used with FPSC Classic only. FPSC Reloaded (Game Guru) is completely different than the original FPSC so it cannot convert levels from it. Also, the levels in it are generally more graphically intense and larger, with terrain etc.. which just wouldn't work very well on many mobile platforms.
You should however have no problem running the converted levels in AGK2! It is designed to allow you to quickly piece together your 3d world in FPSC and with a few clicks have it running in AGK.
I can't really comment on the use of 3D World Studio in AppGameKit and FPSC, im sure you probably could use your levels, but you would have to manually convert them to the correct format and do some work yourself. But i am not speaking from experience.
Hope this helps!