Help! Putting in A Pillar Patch

[Jakes-66-K10]

I'm really discouraged, and not sure where to go with this repair. Very disappointed in the quality of patch panels, and what it takes to get them in...

I'm worried that the floor pan and lower cowl piece I've installed are incorrectly aligned. I had to do some cutting and reshaping just to get them to match up with each other. Now I am finding that when test fitting other pieces that connect to these, something is way off.

First, is the lower A pillar patch, which I've been trimming away to get to fit. If I align the top to the A pillar, the bottom sticks out half an inch.