I can see where there is a stop in the front trunk hinge to keep the trunk from opening to far, but can't find the stop in the closed position.

My trunk does not seem to close all the way down and flexes for the latch to catch. The rubber adjustment stops are out to make sure they are not the cause. It feels like it's stopped at the hinge but can't figure out how to adjust.

There’s no stop on the hinges. The only stops are the round rubber bumpers in the front corners, and they are adjusted by twisting them

Any chance you installed a new hood gasket ?
They tend to keep the hood a bit high.