I am using ajax_command_after() to insert content in-between table rows
apparently i cant alter the behaviour to add an ID to the returned contents wrapper DIV

is it possible to insert DIVs in-between each row using some sort of table equivilant to hook_form_alter (perhaps its called hook_table_alter)?

Would hook_page_alter() be a good solution or would this be using a sledgehammer to hit a nail.

I would use this to insert empty DIVs with unique IDs in the spaces where ajax content could go and replace ajax_command_after() with ajax_command_replace()