I've been using 531 for a long time. And I did IF for over a year sort of like the lean gains approach.
IMO you need to eat a decent amount of carbs everyday and every meal except maybe breakfast. I'm still having a protein/fat breakfast. At our ages stress is most likely the culprit. Cutting back on that in all aspects can help us get back on our feet. That would mean going back to the 4-6 small meals a day. Doing this will take stress off your adrenals. When you go a while without carbs your adrenals put out the hormone in charge of gluconeogenesis. Either way this will occur to some extent, but it will be much less when you are supplying yourself with carbs on a consistent basis.
As for exercise, 531 is a great program and I suggest you stick with it. Even though it would suck, you could trim it down to the 2 day template and just do the prescribed reps for a while. Thats what I'm currently doing, and I took a complete month off before I started (am also only using 85% training max). I'll be taking more blood work sometime the next 2 months to see what progress I'm making.
I do eat somewhat paleo-ish, but I have added oatmeal back in and am doing just fine. My main carbs are white rice, potatoes, oatmeal, and a banana most days. Also, don't underestimate intra workout nutrition. Drinking protein/carbs/BCAAs intra can also help take stress off the adrenals.
I know this is not all very well organized, but hope this helps more. In short, find ways to relive stress in all areas, eat in at least a small surplus everyday, and get carbs in consistently. Oh, and get some legit sea salt like celtic grey or himalya.