Just finished checking our roster looking for any incorrect handedness issues after seeing these above quoted posts, and it looks like there aren't any other errors aside from Logan Morrison should throw lefty.
So, there's no need to restart a franchise or wait for a new version, you can just change Ellsbury, Gardner, and Morrison.
I'm not sure what happened with Josh Wall but he may have been like that in the roster update we started with since we didn't do much with free agents because they all retire at the end of year 1. Didn't make much sense to waste much effort on them.
I also fixed Kyle Higashioka thanks to a tip from ShowTyme. The Dayan Viciedo exorcism was successful and a clean version (no stats) of Higashioka is in the vault (PSN = KeepChooglin). You can import him in over the tainted version.