When and how should I check on how my mineral absorption is going?

I typically recommend monitoring progress by keeping an eye on their thyroid markers and their ferritin level. It's good to get blood testing done every 3 or 4 months at least. It's also a good idea to re-do the hair test every 6-9 months to check iodine, selenium and molybdenum status.  

There's really no point in re-doing the Organic Acids Test until your TSH, iodine, selenium and molybdenum are all within range. Because if someone still has subclinical hypothyroidism, and they are still deficient in those key minerals, then we know that they also still have inadequate Flavin Adenine Dinucleotide and Flavin Mononucleotide. Even without running another Organic Acids Test, we would know there is room for improvement just by looking at the blood test results and hair test results.

So I recommend blood testing and the hair test to monitor progress, and then another Organic Acid Test once TSH and the minerals are within range. I personally run an Organic Acids Test for myself every 12 months, and I generally recommend my clients do the same. If you want to monitor progress more carefully, you could run one every 6 months if you want. Some people do that, especially earlier on in the protocol.