I find it takes ME a bit to get back into homeschooling after we've taken a break.

I have to retrain myself not to answer the phone during schooling, and to really focus on the schooling during that time. The timer has become my friend instead of my enemy, and I've found it to be the best tool to keep us all on track. I vary the times as necessary, sometimes giving us extra time when needed, but as I hear the timer beep if I am in the middle of something when I should probably be near the end of it, I hurry it along and finish. This keeps me from being the one to drag out the day. I am jotting down Leah's idea to note how long each box is taking and see where we might be getting off so I can better make my schedule and tweak the order of boxes and times as necessary. I also agree with sharonb that doing the boxes in the same order each day makes a huge difference. It helped to train my ds to check off the boxes as he completed them, and I gave him a schedule of the order of the boxes too, so if I was busy with my other dc, he could read the next box and get everything together and possibly start on his own until I could join him.
Last year with PHFHG, I started the year beginning the school day at 9:00 AM, having a long recess/lunch break in the middle, and ending around 3 PM. I had audio books and computer time in that plan as well. About a month into the year, I took the audio books and computer time out of the school day and moved them to the night/weekend. I also started at 8:15 and was able to finish by 12:30 PM. This was about a month into the guide. So, I guess that's when we hit our totally smooth stride, though I'd say we enjoyed schooling and finished each day before that - the second schedule was better for us.
If you have any extras, I'd take those out for now, and also play around with the order of the boxes. Once you settle in on a good order, giving your child a schedule for the order of the boxes might help. It sounds like you had a good first week, and each week will just keep getting smoother and shave more time off your day.
In Christ,
Julie