First off, as long as your frame doesnt protrude to far over the edges of the LCD you will be fine. You can usually look at the lcd and see where the part that displays the image starts.
Read and follow the air path layout in the guide. You will need cool air to flow over the LCD to keep its temperature down.
Sorry but I can't answer your lexan question.
Yes the rails that hold the LCD can be made from wood. My suggestion would to just spend some time browsing through the forums and looking at peoples PLOGs for ideas. The search is also a very powerful tool to find specific information.
A lot of people base their box width and height off of the size of thier LCD. Find the demensions of your stripped monitor from others who have used it or strip it and measure it yourself. Then depending on how you decide to mount it will also determine the demensions.
Good luck with your build. My best advice is to read, read, and read some more.