If I try to update my subversion repo, it says I must run cleanup. If I run cleanup, it says a file is missing. (I deleted a MASSIVE directory of files that failed to commit
I've been in similar situations. Have you tried running cleanup from the root of your workspace? I know sometimes a cleanup from a child directory (where the problem lies) doesn't work, and cleanup from the root of the workspace does.
If that still fails, since you had deleted a child dir somewhere. Try deleting 1 level higher from the child dir as well (assuming that is not the root), and re-trying update and cleanup.
If cleanup attempts aren't succeeding at any level then the answer is unfortunately checkout a new working copy.