My process for creating a runnable JAR from a project with many libraries with Eclipse has been.
Export > Runnable JAR > Select launch configuration > Packag
You're facing two issues one seems major and one is minor:
The solution of both of the issues lies in the way you are building the artifact. First of all, remove all extracted *.jar then add all the jar's from the available elements pan as shown in the figure.
It is obvious that adding packaged(compressed) jars only, will decrease the size. But it also solves the signing issue. For more explanation, please have a look at this article. I'll only quote one line.
It's probably best to keep the official jar as is and just add it as a dependency in the manifest file......
It seems that some of the dependencies are signed and repackaging messes up the META-INF of your project.