For (1), we don't have any working examples using Errai in an ear. This might be a problem for Errai marshalling. The marshaller has to reference all the portable types in a single class, so I'm not sure where you could put this class such that it could be loaded properly, particularly if you had portable types spread across several WAR files in a single EAR.
For (2), I know we have a different version of JAX-RS which has to do with GWT compatibility (but we are currently working on upgrading this). But what other versions differences have you found? In general, anything that is provided by WildFly, you are probably safe to use the WildFly version and override the version in errai-bom.