1. How do I set the unused FD cells to my desired color?

Have a look in Basic Functions
under the Heading FD Preferences
(although it is not quite finished)

And have a look at the Appearance page.
Look under Color settings.
The settings for the cells are there.
You have cell colour and selected cell colour as well as other color settings like border and so on.

You can also enter the value "transparent" manually.
You can see details how to do this in Mafi0z Tutorial
Fully Transparent Logos

If you have the setting in Preferences/General "Empty Cells" un-ticked the unused cells will not be visible. So to see them you need to tick this option. (show empty cells)

2. What happens when I exceed the number of cells on a page?

Basically if you keep adding items by "adding to Fast Dial" the number of cells will increase automatically in the Group you are saving to.
The number of cells will increase and over-ride whatever setting you might have set in the Group Cell Properties for that Group.

In the group cell you can also set the number of cells that you want in the group by going to Properties (right click on cell) and then by changing the value in the Quantity Field. Numbers greater than 10 can be entered manually. It is always advisable to keep the unused cells to a minimum.

3. My understanding is that a group is a pointer or link to another page that will contain like topic links. Is this correct? And, is there a way to customize a logo for a group such that a group title can be displayed in the cell?

Yes to your first question.

If you have a group cell, you can go to Properties for that Group cell and enter in the Title Field the name of the Group
Have a look in
Basic Functions
under the Heading:
Creating Groups
The title that you select for the Group Cell will be displayed in the "Back Arrow Cell" of the Group and also in the Tab.

You can also by ticking the Custom Image option in Properties, browse for an Image for your Group Cell.

4. Is there a Tutorial or guide for how to build custom logos (specs, tools to use, etc.)?

If you look at the top of the page you will see the word
Tutorials.
These are the Tutorials on this site for the subjects that you ask about.

5. I noticed that some of the available logos are build such that the background color is derived from elsewhere, i.e. transparent. However, I've not been able to get this to work. Is there a problem using this in FD 1.9 or am I doing something wrong?

I am not sure what your question relates to, but Transparent logos will not display as Transparent in Firefox 2.
There are good Tutorials on the subject of logos by Mafi0z in :
Basic Functions
Fully Transparent Logos
Using Transparent Logos

2. If I understand correctly then FD will automatically expand the number of cells and presumably decrease the size of each cell and I presume this happens on both the groups and the root?

Once you have set up your cell size,(I use the fixed option) the cell size will not alter when more cells are added to the group/root.

2, Does setting "fixed" limit the number of cells on both the root and the groups?

No
The setting fixed relates to the cell size
Try playing with that
Set a cell size and compare fixed and unfixed.
I prefer to use Fixed,

2. Reason I ask is that I would like to limit the number of cells that would be contained on a "page" in order to keep the cell sizes (number of) at a useful level for my eyes and my normal browser window size.

look you need to play around.
Use the fixed setting and increase the size of the group cell until you are happy with it.
Two abreast works quite well so a setting of 2x6 for example for the page.
Increase your cell size to fill the width of your window.
Play around a bit

It is all quite flexible and fun to set up and play around with.

3. that worked as described however, what I was looking for was a way (for a group cell) to have the title appear within the image part of the cell (like it was a logo) as the title information at the bottom is harder for me to see

I understand what your saying.
There are some Logos with words on them
However you can increase the size of the Text Font that you use in the Title by going to Preferences again and increasing the Font size. This helps a lot. You can also change the Font colour if you wish.

I do not understand your "quirk"
Are you not using Firefox/Fast Dial to cover the whole screen ?
I have not experienced this problem.
You can tug on the edge of the Properties Menu, so maybe you could tug it to the shape and place you want ?

Some additional information. I run a 2 monitor system with monitor 1 on the right and monitor 2 in the center. If FF is on monitor 1 the menus appears under wherever the mouse pointer is located, however with FF on monitor 2 (both tests were with FF not in fullscreen mode) when I right click the mouse the menu appears to the left of the FF window, which depending on where the window is located may not be visible. Also, both monitors are set to the same resolution but are of different sizes with monitor 2 larger.

Will do from now on in. Most of the other forums want you to use "reply" as it keeps the topic's thread together. This software must work differently. Thanks for all your help, I'll play around with things awhile to become more familiar with the software and see if I can find out how to report the display problem.