I had an intermittent limp mode issue for the longest time. I could even fix it just by slamming the drivers door on occasion. Since you’ve done so much work to your engine, I would check the place I found my problem. The underside of the main harness as it crosses the intake manifold. In my case, the engine cover has squashed some wires to the point I had a bunch of shiners. After some wire repair, the issue was fixed. It’s worth a shot as I found that the main harness as it’s pulled across the manifold is very tight and rubs in several places, especially if you’ve moved it yourself. You’ll never get it back perfect. Thats my experience.