1. Yes. I was trying to reproduce the issue you were having going over 42 in size with a test clickbar with nothing on it. I couldn't make it show on my character set. I then re-sized my existing clickbar and was able to bring it up to the max of 256x256.

2. Check Link -- I needed to re-size my working set of clickbars. I didn't use the wizard.

3. I am using it for the abilities I am too lazy to bind a separate key for.

Lax has documentation on it listed here on the wiki, though it's a pretty straight-forward concept. Create a keymap in ISBoxer and tie the clickbar button to it. If you have any trouble man just keep posting here or come to the ISBoxer IRC chat.