Sorry you're having a stressful time OP, I have been there and done that with school transport and school too and it's difficult and hard to see a way to suit everyone while keeping the child in question and their needs at the centre of it all.
I would suggest you speak to your council's home to school transport team. I know their level of understanding, helpfulness and ability (or will) to accommodate vary hugely from one to the other, but it might be worth giving it a shot.
Our LA have - over the years - picked and dropped off variously at a childminder's house and workplace after much arguing and justification. I know they are difficult when there is a difference in distance. Thankfully, we are in a position now with work etc. where he can be picked up and dropped off at home. They might also agree to switch his place in the pick up schedule but I appreciate this might be distressing for him and might also cause difficulties for other parents and carers who have made their plans around their child's current approximate timings. He may be able to be picked up a bit earlier or later, of course this is case dependent and you shouldn't really have to ask for this as your daughter's school should be accommodating the changes they see fit, but it might be worth a try.
Alternatively, I'd also be asking the same team about your daughter being eligible for transport, if you think she'd cope with it. Having an EHCP makes it an easier request to make, but as the situation stands her additional needs should qualify her and you can also state your son's needs and disruption to his routine and school life as an extra reason for the request when they ask for additional information on the form (or when you speak to them informally, beforehand). It's all worth a try IF you think either of these things would be acceptable and suitable for your child(ren).
In terms of the school, it does sound like they're trying to find ways to help her settle and that is commendable - leaving aside the logistical difficulties for you. However, the part time schooling and unconventional methods are only OK if they're acceptable to you and working for your DD.
Wishing you luck, and I hope the advice and support you've had outshine the ignorant and sometimes weirdly jealous comments. It's a really hard one to understand unless you've been there, but those of us who have get you.