This website has some great articles about troubleshooting and quality control; emphasis on flat-stock printing.
The author (Mike Young) has also published a book called "The Register Guide", a bit pricey, but goes into substrate, screen prep, tensioning, squeegee details, press setup, printing, troubleshooting, etc., in more detail than you would expect; the focus being on flat stock printing. Some of the articles mentioned above are derived from the book. The book is not listed on the web site; you will have to e-mail him (contact info on his web site) for ordering details. I saved a boatload of $$ discovering and fixing stuff I was doing (and about to do) wrong from the information in the book.