I am not certain exactly if this feature of AC would help you, but I can think of two possibilities. Maybe you have thought of these already and they just wouldn't be feasible for you.
1) In a patient chart under "Summary Sheet" to the middle right is "Tracked Data/Flowsheets." You can input specific values you wish to keep track of.
I use these fields to keep abreast of health main items during my routing annual physicals. I track colonoscopy, DRE/PSA, mammography, bone dens, paps, cholesterol. I don't record the values of the test but rather I indicate the date the test was done and when it is due next.
2) Import an Excel spreadsheet into the "Imported Items" section and use this to track the items for each patient that you are currently using pen/paper to track.
These are just my thoughts, but as a F.P. I don't really understand what exactly you are tracking or exactly how you need to track. So maybe these ideas are helpful, maybe not? Let me know if these solutions fit your practice model.