Tracy,
The ladies have done such a good job of helping you with some ideas.

Children can be such a joy and such a responsibility all at the same time. They can wear us out with their quest to be noticed, and with homeschooling going on they are with us 24 hours a day 7 days a week. Or, at least it often feels like it!
As I was reading through your post, I had a few thoughts that may or may not be on target. So, take what I'm saying with a grain of salt.

I'm sensing in your post that your little daughter is desiring one-on-one time alone with you without distractions. I have a child like this at home too.

While it is so thoughtful of you to do a Keepers at Home study and a Mother-Daughter Bible study, both of these types of situations still leave her vying for your attention among a group of people. In listening to what you're sharing about your daughter, I'm thinking that planning for time for the two of you to be truly alone is the ticket to filling her little cup.

With that thought in mind, I'd lean toward having time where you snuggle in her bed in the evening and read to just her and have a little "private talking time". The reading and the talking time could be super short (like 5 min. each). You could get a little devotional for young girls and just read one each evening with her and talk about her day. Or, another thought would be once and awhile to have hot chocolate with her at a coffee shop and just talk.
I know that having her cook with you is one way that you're trying to include her, but if you're anything like me, you're likely preoccupied during cooking and this makes it tough to keep little ones safe in that process. It also gives your daughter time with a mom who is distracted.

For this fact, I often keep the little out of the way when I'm cooking and just have them come and help with the baking sometimes (like when I make cookies or muffins). I wouldn't lean toward cooking time as being a one-on-one time with her. It would stress me out too!
As far as school goes, I would try to do as much of it as you can with your daughter anchored on one side of you with your arm around her and your son on the other side with your arm around him. I'd snuggle up with both of them during this time. I'd make sure your daughter's phonics time is one-on-one with her with no interruptions if at all possible. The rest of LHFHG I'd do with one kiddo on one side and one kiddo on the other. For misbehavior at our house, we have the boys stand in the corner with their nose facing the corner. When they're ready to behave they may come out. If they misbehave again, they go right back to the corner. This is something you could easily do while working with both kiddos without disrupting school too much. Our other boys are not allowed to look at the child in the corner and are instead expected to go on about their own school. If the child in the corner ends up in the corner multiple times in a row, we set the timer for the time in the corner to equal one minute for each year in the child's age at the max.
I would also work toward requiring your daughter to have a playtime in her room each day. All kiddos need alone time and need to learn to play alone. For some it is much harder than others, but it is a useful skill (for your sanity too).

Put some safe toys in her room, books, a CD player with some CD's, a little table and a chair, and probably paper and pencil or markers (as long as she isn't prone to write on the walls). I'd start by training her to play 15 min. on her own each day. Then, work up to 20 min. and eventually up to 30 min. It can be painful to train a child to do this, but for each time our boys come out of their room during their playtime we add 5 more min. in their room right then. This teaches them to not come out during their scheduled playtime.
Last, I would work toward trying not to feel guilty about your time with your daughter. As a homeschool mom you are likely very busy during the day, but you are present during the day. This fact alone is very much in your favor.

I think often as moms we feel we need "quality time" in each and every day with our children, but the fact is in a homeschooling family children get "quantity time" and some of it is "quality time".

Time is on your side, and you will see this bear fruit as you travel further down the homeschool path. You have time on your side to train your daughter, time on your side to just be with her, time on your side to be her teacher year after year after year. Guilt is Satan's burden to us, and the Lord wants to make your burden light.

Don't let Satan steal your joy!

You are working hard to live out God's call on your life. Feel good about that fact tonight.
Blessings,
Carrie