Cut the patch panel to what you need, unless it makes the seams easier to fill by cutting the truck to fit the panel. I cut my cab corner patches to fit the truck; I cut the truck cowl panels to match the replacements. I made my own inner cab corners - wasn't hard, never shows.
From your pics, the cheap cab corners won't cover everything you've cut away (they don't extend far enough inboard). You'll have to make your own extension patch panels. I've heard there are better cab corners available but I haven't seen them in person.
I flanged all my patch panels then read here that the extra thickness of the lap joint may show when the truck is out in the sun, due to differing expansion characteristics. Better to butt joint, but harder to do.
