1) No, there is not a limit on the number of files you can add to a project. I have had books with 1500 or so files process just fine.
2) Joining files together allows you to put more than one file under a single chapter marker. For example, if track 1 thru 15 are one chapter, i can select those 15 files and then join them. Cds themselves are imported as 1 chapter be default. You will have to use the split feature first to make all tracks their own chapter before being able to mix and match tracks into accurate chapter groupings.
3) The maximum part length is for control over how long parts are if the book has to be broken into pieces due to length. There are limitations on how long a book can be and still play on the iPhone/iPod reliably. for instance, if your book is 26 hours long, you can choose to break it into 2 hour parts, or 15 hour parts if you like. If you want as few parts as possible, make sure the part length slider is set at its maximum value.
There is a help document that has a beginner guide located under the help menu at the top of the screen. There is also a PDF version at our website here:
http://www.splasm.com/audiobookbuilder/downloads.html