We've taken a year off of HOD (gasp!) to do Geography but plan to resume next year where we left off and that is at RtR. My 7th grader and 9th graders used CtC last year for 6th and 8th while my 5th grader (4th then) used Preparing. I'm skipping Ancients with the 5th grader so she can be on track to do the Guides in order (and also b/c as a family we read through the OT every year and discuss the history quite a bit). I might have her listen to the MOH audios to get a more solid footing in Ancients. But anyway. My 9th grade son is not doing high school level work in any subject. I've spoken about him on this board extensively, some of you might recall. Things haven't really improved with him. 
We are not pushing him, but working with him to have a solid grasp of the basic core subjects before calling this "high school" for him. Therefore, next year we will most likely call 9th grade for him. I don't think I need to add much to RtR to make it credit worthy for him. I plan to have him read through MOH2 in addition to the Withrow books and Story of the Middle Ages. And, b/c we lean messianic in our beliefs, I will also have him read another book that we own that approaches early church history from that perspective. That should be plenty. As for science, this year was a bust. He got through 4 modules of Apologia Physical without retaining anything. I ditched it and we are not going through CKE Chemistry with him and his younger siblings. I don't care that it won't or can't or shouldn't count as high school credit. He needs basic. Next year he can either do EE Physical or continue with Chemistry using Chem 101 or Friendly Chemistry...whichever he prefers. Does that sound acceptable?
Literature I think will be easy to beef up using some higher level books. I had already planned to do the AiG Pilgrim's Progress Unit Study with all my children so that will add significant "depth" to the Literature portion. I'll add a few more full length novels in addition to the Shakespeare already scheduled and call it Literature. He will continue with AG and do the IEW Medieval to round out the English credit.
For math, I am ordering the new HOD suggested book from Masterbooks. This child has not fully grasped the most basic of Pre-algebra concepts and is struggling through MUS Pre-Algebra. I'm having him go through Life of Fred Pre-Algebra now and he is tolerating it. I think the Masterbook math curriculum looks fantastic and if we worked through the summer I think we can get him up to speed to start Algebra sometime next year.
I think that about covers the basics. Oh...Bible.
We do extensive Bible study as a family. We read through the Torah portions each week and dig pretty deep with those. My children each have their own personal Bible time as well. Currently, he is working through Discovering Our Amazing God by the same publisher as the Rooted and Grounded Study used in the WG Guide (which we loved!). He will continue on to do the Discovering Who I am in Christ book and that should make for a credit. Electives are up to him. At this point, I plan to show him God and The History of Art which would complement the time period very well, I think. He is interested in art somewhat so this should be agreeable to him. I hope. Am I missing anything at this point? Any other suggestions? I am open to any and all. Thanks ladies!