beverett,
If your child is new to HOD and isn't as familiar with some of the skills in the guide that are listed as being independent, then it can take a month or two to get into the flow of an upper level guide. If your guide seems to be going much longer time-wise than what we are mentioning it should take, then there are a few things to check.
First, here is a thread breaking the boxes in CTC down into times, so you can see how long each box took us. It's a good idea to set the timer and write down how much time each box is taking your student and then compare to see where he/she may be going over. Link:
viewtopic.php?f=6&t=3765 
This leads me to my next suggestion.
Second, if you are using a different language arts or math than what we schedule in the HOD guide, then it's good to see if those areas are adding time to your day. It is possible that the 3R's could be extending your day, rather than it being the other boxes in the HOD program that are going too long. For example, in CTC we allot 5-7 min. 3 times weekly for dictation (which is spelling). If you use a different program for that, and it takes more time, then that would be adding time to your day. You can still keep your own favorites, but you may wish to get them down time-wise to something comparable to what we are planning for these areas time-wise each day. This will help in the length of the day and keep you in balance.
For grammar in CTC, we are doing half-speed Rod and Staff, setting aside about 20 min. twice weekly for grammar. For Drawn into the Heart of Reading, we are scheduling it 3 times weekly at about 35 min. a session. For math, we are allowing approximately 30-35 min. daily for Singapore. We schedule Write with the Best twice weekly for 20 min. a session for the writing program. For science, we are allotting 30 min. a day. High school science will take longer, so this will add time to your day. When comparing how much time you spend on each of these areas, you may possibly find some reasons for your day going longer.
Third, if you are having your child check in with you after each subject, it could be that he/she is spending time waiting for you when he/she instead could be working. You may want to group 3 independent subjects in a row to cut down on his/her wait time with you between subjects. Then, follow the independent sessions up with something scheduled with you. At the beginning of his scheduled time with you, check-in with his completed independent subjects all at once. This will cut down on both of your checking-in times but still accomplish the goal of looking over his work. With my older students, I typically check in twice daily briefly to make sure they are on track.
Fourth, check to see what you are adding on to your child's day that is not a part of the CTC guide. Sometimes it's amazing to see how much time the few "little things" we add take each day. If you are adding anything extra beyond the CTC guide (except for a higher level of science and math and maybe a higher level of grammar), I would drop it if it is not needed for his/her high school requirements. The Bible component in CTC is very strong, so don't worry about adding more. Try using the guide as close as possible to the way it is written with extensions and see what happens.
Anyway, these are just a few ideas that may help! We'd be glad to brainstorm more if needed to get you time down to where it should be!
Blessings,
Carrie