I have no idea about the errors on your server.
Updating to bukkit is EASY
1. Get this. http://forums.bukkit.org/threads/craftbukkit-auto-installer-beginners-minecraft-1-0-0.26555/
Don't worry, it installs a load of stuff but it's all safe.
2. Copy the world folder, region, DIM-1 (if you have it), opped players, banned ip's (hehehehe) etc and all it's contents across from the vanilla server's folder, to the bukkit one's. If they're there yet... i cant remember if they get generated later. Don't worry about the players folder.
3. Open the server properties.txt file and change all neccesary fields
4. Double click "craft bukkit starter" (NOT "CRAFT BUKKIT STARTER JAVA 7" OR "CRAFT BUKKIT STARTER JAVA 6" It should optimise java, then come up with a server log, similar to the vanilla's one. I think this is when it generates all the folders such as "world_one, world_nether, world_theend. If so then copy the your previous world folder's contents across, and sorry for getting the order wrong.
5. Also "pail" will come up. Change all the tick boxes in pail to what you want. As stupid as it sounds... PRESS SAVE. lol...
This is all from memory as i'm not on my laptop with my server on. So this may not be EXACTLY right.
Then once you have set it up i can tell you some more, but the most important thing is
6. Go to http://plugins.bukkit.org/#ti=&ta=all&au=&subm=false&pno=0 and download as many as you want. Put them in the plugins folder making sure that the .jar file is loose in the plugins folder.
Let me know if you are actually going to use this info and if it works.