Ok, here's an update on my issues with my site(s). I manually reloaded the latest version of wordpress, overwriting the files there. This got rid of most of the problems. Then it finally clicked - I had been looking for the actual code, not the crap code hidden in the eval that wasn't supposed to be there. Now, I've got to hit each php file and make sure it's clean.
Thank you to everyone who offered help to this lost soul. I will check here and post back once I have gotten thru this. I'm sure I'll have some additional questions before it is all over.