I dont believe they change stiffness on reheating. I've remolded mine several times & having notice any change that way. However, I did noticed that they shrink in length. I ended up with the liner being too short despite buying them 1 size larger to start with.
The overlap can sometimes put pressure on the shins if they are not positioned properly during the molding process. When molding make sure to pay attention to the overlap & make sure that its positioned so that the seam is well away from your shin bone. Also you may want to move the cuff buckles positioning to give you a little more room in the cuff. The intuitions for me had quite a bit more volume in the cuff than the stock liner. I had to move the upper buckles 1 hole over to get more room. Not sure if this will help with your shin pressure problem, but it could give you a bit more adjustable range to play with to find the most comfortable spot.
Also for what it's worth, I would recommend using some neoprene topcaps vs cut up socks. The sock topcaps are too soft/compressable and can result in a cramped fit in the toe area, esp if the liner is a tight fit to start with. When I had my liners remolded last time by Intuition in Vancouver, they have started using double neoprene toe caps instead of just single. It made quite a difference in the fit for me. I was getting major toe-bang before, but no more