Sorry to hear you have been through such a tough time but good news about the baby.
Can you clarify what happened with the flex application, how didn't they follow procedure and what was the outcome.
What had happened to your old job and why weren't you allowed to return to that. You are entitled to return to your original job at the end of leave unless it is not reasonably practicable - basically if it no longer exists. If it no longer exists, they should have spoken to you about that with regard to redeployment or redundancy. they have to give you a job on no less favourable terms and conditions. The fact that you have more responsibilty, travel and workload means that you are on less favourable terms and conditions, particularly if your pay hasn't increased.
Why did they say there would be no job for you if you didn't take that one?
If you can clarify those couple of points for me I can give you some more info.
Based on what else you have said they are bullying you. They are also treating you less favourably than male colleagues in a similar position so probably sex discrimination for that and also with regard to not allowing you back to your old role. they are possibly in breach of the flexible working process too.
You will really need to put in a formal grievance covering every aspect, point by point. Follow their procedure to the letter, make sure you have a resolution in mind (is working from home and more manageble workload enough for you). Don't worry if you have a massive list of things to cover, even like the pay rise aspect - do you have evidence of other people having a pay rise.
You could potentially resign and claim constructive dismissal but I would advise that you follow the grievance route first as its a tough case to bring as you have to prove the treatment was so bad that the relationship was untenable and you could no longer work there. Saying that, you are suffering stress as a result so obviously its bad.
See if you have legal cover under home insurance cover as it usually covers employment issues. Phone ACAS or CAB too and most importantly keep detailed records of comments, conversations etc for evidence in the future.
finally, get signed off again if you feel its too much for you. You can always do the grievance by letter and ask them to deal with it, going in for a meeting if you feel up to it