Rose,
The version of MyEclipse you are running is not compatible with the final 3.0 release of Eclipse, this is in the notes underneath the download.
As far as your errors are concerned, you likely need to navigate to Window > Preferneces > MyEclipse > J2EE> Library Sets > 1.3, and click the “Restore Defaults” button, then navigate to your proejct Build Path and try and remove and readd the 1.3 Library.
The problem is that the library is trying to use files from the 3.8Beta 2 installation, but that isn’t there anymore.
I would encourage you to hang tight until we release 3.8 GA in a few days and just install that with Eclipse 3.0. Also next time you get lockups and failures please come to the forums and we’ll see if we can help, we aren’t aware (nore has anyone reported) any such errors before.