1.) There's no reference other than what's posted on Cato's pages, the Readme file.
http://www.jcato.net/downloads/history/readme5.html
Usually if you get stuck walking through the instructions, you can post a question here and we'll do our best to answer it.
2.) You can't use the utility with *just* the almanacs (at least not to my knowledge) - you have to have backups of the league files as well.
P.S.) The best time to run the utility - at the end of every season. I personally back up my league directory (leaguename.lg) to a Zip file at the end of every season, at the point where the schedule shows the "Proceed To Next Season" button. I then backup these Zip files. Alternately, you can back up just the .CSV and .HTML files that the OOTP Utility program needs to create its database, but these files should be saved at the same point - the end of each season.
With regards to the null error - check all the options on the File | Options screen, on the General and Awards tabs. Actually, just check all the tabs to make sure all fields have a correct value and aren't empty. If they're empty, fill them in with something appropriate. Most importantly, make sure all of the paths to your league file and other directories are correct.
If everything in there was OK to begin with, then check the Enter/Edit Team Info screen to make sure everything is filled out.
With regards to the abbreviations changing, - I haven't done this specifically, but on the Readme page on Cato's site, scroll down to the "After Importing Data" section, under step 1. That should give you all the info you need.
Hope this helps!