First up, I would like to say that I am not excusing his pettiness over the kiss issue, nor the rudeness - it's not on, and it needs to change. However. I have a chronic and painful condition too and mornings are awful for me. Try as I might (and I do!) I occasionally end up snapping at DP, then by lunchtime feel bad about it because the tablets have kicked in and the fog has cleared. I shouldn't do it, and I always apologise, but none of us are perfect.
Secondly. I have a lot of sympathy with his insecurity, both regarding the work issue and the getting up in the morning. I am very funny and touchy about this. We live in a society that sees anyone who's not up by 8.00 as lazy, and if you get up any later you don't get to complain about feeling awful. Even if it's not said, even if you're with sympathetic people who understand why it is hard for you to get up in the morning, there is a societal pressure and it has made me go a bit funny in the head - I get paranoid that I am lazy, that I should just get my act together and stop whining and I'm just a horrible person. That also extends into my condition in general - like your DP's ME, it's not visible, not quantifyable and very variable. On days where I don't get anything done, or not as much as a healthy person would, I feel bad about that - what if I'm actually just whiny and everyone feels like this? It took me a long time to realise that's not true, and my partner's support was very valuable in that - he helped me feel better about myself when he pointed out the last time I worked a full time job I got signed off after 6 weeks because I could no longer walk.
I think your partner needs some help to work through his feelings of insecurity and being unable to work as hard as he used to, perhaps one-to-one counselling might be better? Group counselling is my idea of hell but I've found private sessions helpful in the past. Simultaneously he needs to work on not being rude to you and finding productive and proactive ways to deal with the issue. He feels godawful in the morning, there's probably no changing that (although it is worth investigating if that is in fact the case - could he see a GP, perhaps to ask if there's any kind of long-acting tablet he could take at night so he doesn't feel so dire when he wakes up?) so between you you need to find ways to work with the unchangeable aspects of the situation. That may, in fact, involve you leaving him alone in the morning until he feels well enough to hold a coherent conversation, and him learning to say 'sorry, I feel awful, give me an hour' rather than barking at you.There must be solutions - can you write down the information he needs to have before you leave, rather than relaying it verbally? That way he can look at it once he's conscious enough but before he needs to know it.
Finally - I really don't want you to feel like I'm picking on you, as I have a lot of sympathy (I know how hard living with me sometimes is for my DP) but when you say things like 'I have to hope he won't play on this to get a lie in', if you are saying that to him or giving off that kind of vibe that will feed into his insecurity massively. If my DP said that to me or implied it I would be a twitchy paranoid wreck for a week because the idea that people feel that way about me and the niggling worry that it's true and I'm actually just putting it on and should get a grip(even though all rational evidence tells me that it isn't) is more or less my worst fear. It's pretty much the least helpful thing you could do. I think you are going to have to go into this quite gently - make clear that his behaviour is not acceptable (because it isn't, and I'm completely with you on that) without making him feel even more insecure and defensive than he already is because it'll be counterproductive; while at the same time also trying to empathise with him because, let's face it, his situation is pretty shit.