fitting floor patch panel

[jd4300fel]

My question is fitting the drivers side floor patch panel.
I have to replace the cab support/floor/kick panel/rocker.
My problem is the indent for the bolt that goes to the cab support does not
line up with the bolt hole on the support that goes from the back of the cab to the fire wall. I am off about .5 inch. It looks like I need to take a .5 inch
out of the whole floor panel between the rocker panel and the indent. how do I solve this? Do I cut the indent out, in an approximitly (sp) four inch square get the floor lined up, then line up the indent and weld. I am almost sure others had to deal with this type of problem?
I did not have this issue on the passenger side.

thanks for the help