I’d avoid joining objects together just yet if you can, since that step comes later. Try going back to the first frame when everything is as it should be, and unparent everything, delete the mesh that was created by applying the modifiers, and remove the modifiers. That way you can do the parenting and mirroring process again with a fresh start, since it sounds like something got mixed up along the way (parenting to the wrong objects or applying the modifiers too early). Hope that helps!
