put some sturdier crossmembers on the frame. These trucks simply aren't meant to go through what we tend to put them through. I haven't had the same issues with the windsheild, but I have had my body/frame flex enough for my fuel door to pop open several times, and the latch goes into the body almost 3/4" of an inch.
Yours must be a 4Runner, I can't see that happening to a p/u bed. I wonder if the 4Runner frame and body are a little more rigid than the p/u's--------Hans