Add this to you jar block in build.gradle. Depending on what jars you embed, there might be some that need certain entries in their META-INF\MANIFEST.MF; add those entries into your mod's META-INF\MANIFEST.MF. Also you might have to instruct shadow to remap the embedded jar's classes into the package of your mod.
from configurations.embed.collect {
it.isDirectory() ? it : zipTree(it).matching {
exclude 'META-INF', 'META-INF/**'
}
}