Lightwind - your love and concern for your son are palpable and shine through your posts. I'm glad the support on this thread has been helpful to you. I don't have much in the way of practical advice for you - but I would like to say that it sounds like you're doing a fantastic job, and I hope you can try to be patient and loving and forgiving with yourself as you really deserve that. You do sound like you're giving yourself a bit of a hard time about it (which I totally understand, the feelings of inadequacy and frustration and so on) so when you're feeling self critical maybe it would help to remind yourself of a few things:
1), that you are, as you say, genuinely suffering from a chronic illness which makes this particular stage extremely challenging for you;
2), you are not a failure as you have done incredibly well to overcome your illness enough to be a mum in the first place and to be as loving and happy a parent as you sound;
and 3), there is nothing particularly uncommon about a 3 year old - especially a boy - still being in nappies these days, so where you are in that sense is actually pretty normal, so take that time pressure off yourself if you can. (And just throwing away soiled pants is also not uncommon!)
I hear you that you're worried that your issues are holding him back, and he's picking up on your anxiety - and that may be; but you can only be the mother that you can be. And you are the mother that he loves and needs, the mother who gave him life - not some perfect cardboard cut out one who gets everything right. No one gets everything right; everyone's bound to pass on some "stuff" to their DCs because everyone's got baggage of some kind. Whether they're aware of it or not. You at least have that awareness and so are in a position to minimise any negative impact on him by compensating in other ways.
I really don't know enough about your condition in general, and yours specifically to be able to suggest what would help but given that phobias are by nature extreme (one thing I have heard about OCD is that sufferers can really feel as if something truly dreadful will come to pass if certain things happen/don't happen the right way, to the point of fear of death, don't know how true this is for all cases) then it's really not surprising you're at an impasse. You shouldn't be comparing yourself to other people who don't have OCD, you need to be comparing yourself to where you were before you were even able to have a child, so you can see how far you've come, and what you have dealt with. In that context, if your DH has more success in this area than you, it doesn't mean at all that you're a failure, just that you are ill in a way he isn't.
Is there any chance at all he can take a week or two off work just to stay at home at some point, and then he can take charge of this? Or if not, would finances allow you to actually employ someone to come in and mangage it for you? Gina Ford (not that I'm a follower!) has loads of case studies of working with families and sorting out potty training for them, so obviously this is something that people do even when they haven't got a phobia; you would be more than justified in doing this in your situation and it wouldn't mean you were failing or welching out of what you signed up for. It's just delegating. You're still taking responsibility for making sure it happens.
And if that really isn't an option either, I am sure you will work it out one way or another, in your own time. Someone who goes through that much just to have a baby is someone who finds solutions to problems, not someone who gives up. I think I may have laboured the point a little 
but I really do hope you can be a little bit kinder to yourself, and I wish you lots of luck.