I hope you made a backup. I've done several of these and it's no picnic. There are a number of things that have been issues. Ranging from PHP memory and execution time limits to the just strange. Since a history of what has or hasn't been done to your setup is nearly impossible (unless you have total recall of everything). So really all the prep-work is really important. Backups, converting to UTF-8, database coalation, table optmizations, etc. I recall my upgrade script taking over 2 hours to run when going from 1.9 to 2.0. Also instead of making a backup, I think I was using a copy of the site, database and data, and put my original site into maintenance, so when I made the switch to the migrated site copy, there would be no missing files/forum entries/etc. I would also recommend to copy you LOG table to another database and wipe it from the soon to be migrated site. That LOG table was what took the longest to migrate, and has been pretty much useless to my sites as no-one really uses it. Go into your XML DB editor in development and execute any SQL DB fixes you find there. These things should help you smooth out the bumps during the upgrades. Also a progressive upgrade is recommended. I would go from 1.9 to 2.0(latest stable) then upgrade to the latest stable version of every branch. I know it's alot of work, trust me I know, but it's what has work flawlessly for me. Other might feel differently on the matter, But my motto is better safe than sorry. Plus once into the 2.0+ versions the upgrades are a sinch. Good Luck.
Thanks for your reply Frank. I did make a backup, but what it included, I"m not sure.
Are you suggesting that I go back to 1.9? If so, how would I do this? I haven't found any documentation on how to uninstall moodle.