No I wouldn't expect the font changing options to be within the preferences dialog. Look in any word processing app or something else that lets you change the font and you will usually find that it is in a "Format" menu or something. "View" makes more sense in mIRC as there wouldn't be enough options to fill a "Format" menu.
To explain how to change the font in all windows I would say this:
1. Look in view > font and decide which font and size you want. Make a note of these.
2. In the box you usually type messages in, type the following: /font -dz "(name of your chosen font)" "(chosen font size)"
I agree that there should be a built-in GUI method of doing this, however. I guess it's sometimes hard to see something from a newbie's perspective when you've used the client for a long time.
Point taken with window positions
