Brian, if your LH is 1.3, then that would in most cases present secondary hypo. Like I mentioned, from an observational standpoint it seems like men with primary hypo tend to have the real low baseline serum numbers, but "not always", as your numbers apparently can attest to. It would be good to have the doctor review that with you so that you are up to speed with your diagnosis and treatment ...
On the Free Testosterone ... No worries on that, the percentage will stay relevant to your serum level. You're currently a little over 3%. So, if you were to get your serum up "say" in the 600ng/dl area, your Free Test will probably come in around the 18 to 19 range, +/- depending on factors like SHBG and a little bit on albumin, which 'shouldn't' deviate tremendously.
So, if anything, keep the free testosterone thought in mind as your therapy program develops. I also have around 3.2% on free test, so it doesn't take a lot of total serum to achieve optimal results. You will see the majority of guys focusing on that total serum number, really not knowing the free & bio available side of it. You will have a much easier time managing your program if you pay attention to that aspect of it, plus of course managing/addressing other factors like E2, adrenals, thyroid, D3, etc..