Rumors are that Jack was molesting Jonathan and his actual cause of death was from suffocation when JY fell asleep on top of him after some rather intense love making. But by a stroke of luck the coroner was jewish and agreed to cover up the sordid affair between JY and Jack after Miriam promised to give the coroner jacks gold teeth, six foreskins, and $1500 in sheckles. Shortly after his funeral Jonathan tossed on his mothers dress and became romantically involved with Miriam as a desperate attempt replace the emotional pit left behind by Jack's death. Jack's lasting influence is why JY is so obsessed with dildos and sticking things up his ass. The rest is history.
(this may or may not be true)