I would not delete anything manually (except the contents of /core/cache/). You only want the software (be it FTP or the OS) to handle all the merging for you.
What OS are you on? If you are on a Mac like me, this is absolutely vital:
http://rtfm.modx.com/revolution/2.x/administering-your-site/upgrading-modx#UpgradingMODx-MacOSXUsers
Are you able to restore your site to a pre-upgrade state? If you can, then I would recommend doing so, and pulling down a local copy and do the upgrade locally, using the merging techniques in the article above.
If that works locally, you can then push the upgraded files and DB up to the server over FTP.
I wish upgrading Modx were easier, but, currently, that whole merging procedure is absolutely vital. Maybe someday the good folks at Modx will give us a simple package-based upgrader utility. But in the meantime, the article above is good, and just be sure to absolutely understand the merging part.