Hi Mark,
I do understand, and I had more or less the same concerns when I started out with css, about 4 years ago. Here is a site I made back in 2005, before I was able to use css:
http://www.vjgk.no/index.html. If you view the source code, you will find similarities to your own sites: nested tables, fonts, sizes and colours all in the same file. Maintenance was a real pain in the butt!
When I started learning css, what I did initially, was to create a style sheet with only the fonts, colours and sizes, keeping the tables still in the html file. That way it was not too overwhelming. After becoming a bit more adventurous I also added in some properties for the tables, paragraphs and such. You can see that if you click on any of the sub pages of the same site and view the source code, and also if you view the
http://www.vjgk.no/mainstyle.css. I would have continued the transformation of this site, and most certainly made a new design, if it hadn't been for the fact that I moved away from the place and they wanted to have someone local to do the website (with the sad result that nothing has been done since I left...)
My main message to you is, that you don't have to stick everything into the css file right away, but do it gradually. Then you will get used to that way of thinking.
Now to your question about 100% width or not. A lot of sites were designed for smaller screens just a couple of years ago. Take that site I mentioned above, which was made for 800x600 px. Now, if that is viewed on a large monitor, it definitely doesn't look good. That is what happens with widths given in %. What you could do instead, is to set a fixed width, like e.g. in the range between 800 to 1000px depending on the screen resolution of your likely audience (you could ask people within your parish what monitor size they have). When I create sites now, I usually use 900px or 950px width.
I hope it helps, and yell back if you need more help.