Am I expected to memorize every number of every puzzle if I want to solve it or is there an index (preferrably offline version)?
Yeah there is a menu under "File" in the upper-right that has the puzzles broken down into categories. There are images for a lot of the puzzles so you can look at the image in the menu to select them. You're right though that sometimes it can be hard to find the exact puzzle.
Last time I checked the installer didn't download every image available. If you want all available images, I have a zip of them at http://www.brandonenright.net/~bmenrigh/gb_images.zip
Also, can the click-for-CCW be reversed? I find a CW left click to be more intuitive
I suggest you get used to it. Once you do it feels very intuitive. If you can't get used to it, just swap your mouse button settings while using the program.
I suppose it wouldn't be much work for Gelatinbrain to add a check-box to inverse the mouse but any additional settings and the interface will be too cluttered.