@Mitch
Indeed there are some bad documents out there, most notably the one from MAI/TERON.
I found Nerps site to be excellent, as well as the article at IntuitionBase.
I documented some of the rough spots in an article with photos here
http://www.ncscaug.us/ua1page1.htmThe erroneous serial port pinouts have been corrected at the two websites listed above. And are shown corrected in my article.
The "unusual" USB pinouts are documented in my article.
Instructions on how to adapt the smaller IDE connector to support full sized drives are also shown, with lots of pictures.
The proof that my article is right will have to be that the computer I built in those photos has been in use every day since then, and I'm writing this on it now.
Relax, the resources you need are all around you.
Take a deep breath, ask questions as you go, and we'll have you back in gear in no time at all.
LyleHaze