Liz,
I'm seeing two main parts to your question, so I'll focus on the learning to read and follow directions part of your question first with this response, as I believe this is a different area than overall comprehension.

Learning to read and follow written directions is a skill that takes time to develop. Just as with any skill, you'll see the most improvement when the skill is worked on daily. Some kiddos do better with written directions than others. Those who automatically follow directions better are typically kiddos who are detail oriented or who are very systematic!

I am a direction follower, and my husband is not!

However, my hubby has learned to be more of a follower over time.
Usually, kiddos who struggle with following written directions are those who haven't had to do it on a regular basis or have learned to get by without this skill. They learn to skim or wait until someone tells them what to do. In homeschooling this is often an overlooked skill, because when teachers have fewer students to oversee, we often read the directions aloud, do the reading for our kiddos, and make sure they have followed every direction. Come to think of it, it is also an overlooked skill in the classroom, as classroom teachers do this too!

Either way, consequently the students rely on us for this skill. As parents, we likely ask students to follow written directions in sporadic cases, like the example you gave when children are baking, but the steady practice is what will bring improvement.
Within HOD, as you work toward having your child do the boxes marked 'I' independently and take time to train her to do it, you will see her begin to take over the direction reading and the work that goes with it. Begin by having your child read the directions out loud to you, instead of you reading them to her.

Then, have her do as much as she can by following the directions without you jumping in to fix what she's missed. If she isn't sure what to do, direct her back to the directions with your finger under the first direction. Have her read the first direction aloud to you and follow it. Then, have her read the second part and follow it, and so on.
When she is done with a box of the plans, have her read the directions for that box out loud to you to hopefully catch any parts of it she may not have followed. If you can still see that something is missing from her work that was in the directions, run your finger under that part of the directions while having her read it to you. Over time, she will learn to do 3 important things that will make her a better follower of written directions. 1) She will read the directions through before she begins. 2) She will refer back to the directions when she's not sure what to do. 3) She will reread the directions at the end of her work time to see that she has followed them all.

You could even write these 3 steps on a card and post it for her to follow on her own eventually. Just be sure that your days of reading the directions to her are waning, until you no longer do it at all. I know this seems like a lot of work at first, but it is work to learn to follow written directions.
This is such an important skill and one that takes time to develop. It is what helps a child gain independence and is integral to so many parts of life! Yet, it is an often overlooked skill and one that we as parents often love to skip to just "tell the child what to do because it is quicker". You're not alone in finding the progression takes time, and with certain types of kiddos it can take quite awhile! Blessedly, the HOD guide will incrementally train your children in this skill as the student come up through the levels, if you allow them to read from the guide more and more as they come up. Since you've jumped into a higher level of HOD with your daughter, you can expect it to take some time for her to develop this skill. Just be encouraged that as you systematically work on this skill, it will come!

The difference in my own boys from guide to guide is tremendous, so do not despair!
As far as overall comprehension goes, DITHR, oral, and eventually written narration practice will make a huge difference in comprehension. It takes time to see the change, but those are the best means toward better comprehension from lengthier readings.

These things are built into to each of our programs and will improve comprehension over time.
Blessings,
Carrie