Alison,
After I posted, I see that my3sons and I were typing at the same time with a similar thought.
Thanks so much for typing that all out! Although, I must admit that the "I'm feeling your pain" statement was a toughie for me to hear when discussing CTC. It is a guide that is after all near and dear to my heart.
I can see from your schedule some key areas that are resulting in your day going too long. I'll preface my post below by saying that it is going to specifically address how to make CTC fit into the time allotment that we recommend. So, while your priorities may differ from this, and I can understand families differing in goals, my recommendations below are coming from the fact that my purpose is pointing out ways to make CTC work well, so you finish in a timely fashion each day.
From that standpoint, I'm seeing 3 of the first 5 items on your schedule are not related to HOD. In all honesty, I would move the non-HOD items to last in your day as your HOD program is actually covering those areas (with the exception of piano). I realize that your math is necessary to keep

, but I'd make sure to keep the time down to whatever you consider to be reasonable so it doesn't add time to your day. If you look at your schedule out of the first 90 min. of your day, only 20-50 of it (if you count your own math) is related to HOD. I'd shift that so that your son starts with the Bible Quiet Time and then heads into one or two other HOD subjects that he can get done reasonably on time. I'd partner with him and make sure he starts out and ends on time with those first subjects.

You may feel entirely different and look at HOD as less of a priority than the other areas you've scheduled first in your day which is fine too. But, it's good to note then that the other priorities are playing a role in your day going long rather than it all being related to CTC. By changing these opening things, you could have 3 or more HOD subjects done in the opening 90 min. of your day.
When you get to the next subject line number 7, I notice the addition of typing, which is fine, but again will add time to your day. So, I'd likely move that to last in the day away from your other HOD subjects. With number 8, in alternating Rod and Staff and WWTB that time slot will be 20 minutes each day (doing either Rod and Staff or WWTB but not both each day). You're likely doing it that way, but I just wanted to clarify in case. Dictation is around 5 min. or so three times weekly. So, rather than having an hour of language arts all back to back daily, with Reading Dectective instead of DITHR, you could again move Reading Detective later in your day as it is an independent subject that doesn't require you and is not a part of HOD.

That would take that time slot back to 25 min. and allow you to add one of the HOD subjects there that right now is scheduled after lunch. It's also important to note that DITHR is scheduled 3 times weekly as is dictation, so if you're doing Reading Detective or dictation more often than that, your day will go longer.
In subject line number 8, I'm not sure what poetry copywork is because in CTC there's only one short stanza to be copied once a week and the other days are painting and sharing the poem aloud. Perhaps that is what you meant? I wouldn't add additional poetry copywork if you happen to be doing so, but would instead just do what's in the guide for poetry. I'm also stumped as to why your little guy is reading the storytime books to himself? Those were chosen to be read aloud, and if you are already doing a read-aloud with another HOD program, you would skip the storytime in CTC. But the books weren't meant for the child to read on his/her own. So taking that out of his day will help quite a bit time-wise. Were you thinking to use these with DITHR?
The science and history project are written to the student with science meant to be completed independently. So, he shouldn't need you to do those things along with him. I would definitely not leave those for you to do with him after lunch but hopefully these could instead be done on your son's own without you after lunch or earlier in the day?
Last, the narrations are meant to be done right after the readings. So, the written narration should be done right after the history reading. The oral narrations are the same. This is because it is so tough for a kiddo to narrate after lunch on what they read way back in the morning. Unless you're adding more written narration that should only come up once a week in CTC and extra time is allotted for it on that day in CTC by not having a history project that day. So, while it may take a bit to do written narration on that one day, it shouldn't be affecting your whole week.
From all that you've shared on this thread, I'm wondering if your son fits better in Preparing Hearts? I'm thinking that you're having to do so much with him in so many areas that you're using the CTC guide in a much different way than it was intended to be used. You'll know your child best, but I really want him to be successful, and I feel that there are so many skills from Preparing Hearts that he is missing that would really help him with CTC. I am also concerned that there is no way he will be able to be successful in CTC, much less the future HOD guides without that needed foundation. Perhaps, with some changes to the schedule he'll settle in just fine to CTC. Only you can know how much you're having to help him. Another option would be to downshift into doing CTC at half-speed each day, taking more than a year to complete it. This is a better option than skipping things, which will only cause problems once you get to the rigor of RTR.
If you should desire to back up to Preparing Hearts, you can return any books that are unused in exchange for what you need for Preparing Hearts. There's so much more to CTC than being able to handle the reading material and the skills are necessary to complete the activities.

Correct placement in HOD makes all the difference in the world in your day! I want your day to go well which is why I'm brainstorming all of these options with you.

Hopefully, something in here will help as you ponder.
Blessings,
Carrie