Here's an idea of what our expectations are for our 13 year old,

Jobs:
Unpack the dishwasher every morning and put the things away
Clear the dinner table when asked - ie couple of times a week)
Do any other occasional jobs, when asked (these might be things like putting the bins out or bringing a load of washing in from the line).
She also sometimes prepares her own lunch and snacks when she's at home.

Expectations (ie not a job as such but relates to functioning as a human being)
Towels hung up
Put own clothes into laundry hamper
Put own clothes away into correct drawers/wardrobe (after it's washed, folded, ironed etc by a parent)
Bring correct books/implements home for homework, and complete homework/school work to the standard that relate to your own goals
Pick your own things up (in shared living areas) and put them away
Tidy bedroom & attend to own personal hygiene.

As you can see, most of that list is just basic functions of daily living, rather than "jobs". I try to discuss them in the context of how being tidy/organised will make her life easier.

To be honest, I'm not sure if this is a situation where a huge set of rules is going to work. If I were you, I would try to identify a few priorities and just concentrate on those. Basic respect and courtesy is right up there. If he's going to school every day (when he wasn't) then reinforcing that and starting to get some gains in his school work is a pretty high priority, IMO. But do it with some guidance. If he's struggling then the feelings of discomfort can be very strong. The counsellor should be able to help you with some strategies for him too. Remember to focus on the positives where you can. Plan pleasant family activities -esp when his dad is home. Spend some time and find out what things make him tick.

This won't necessarily become easy overnight, but having a few extra strategies to pull out when you need them will help you feel more confident in negotiating with him, and asserting yourself when you need to.