Complete floor, cab corner and b-pillar replacement woes ( with PICTURES)

[CMars45000]

I'm in the process of replacing most of the lower end sheet metal on my truck. I got the complete replacement floor in last week. It wend pretty smoothly, and some of the problems I was anticipated never showed up, like the common issue with the front flange "diving" away from the seam towards the outside edges.

Now I am working on the cab corners and pillars. On there drivers rear cab corner and rocker area, I have some concerns.

With the outer rocker lined up with the door, there is a LARGE gap between the lower edge of the rocker and the inner rocker. If I pull the flange between the inner and outer rocker that will be spot welded, the portion of the outer rocker that extends up the B-pillar is no longer in alignment and I get interference between the lower part of the door and the sill area of the outer rocker.

This issue extends to the cab corner. I am assuming that the lower lip of the cab corner spot welds to the inner rocker, correct?

What ideas do you guys have for dealing with this large gap?