I would HIGHLY suggest using a different program to look at gerber files. It's like having a second set of eyes.

 

Gerbv is a free one.

 

This is the message I get when I try to use the "Update Schematic from PCB" tool:

Yeah, not surprising. You are basically trying to make a walking clucking chicken from McNuggetz.

You can draw the schematic in Eeschema, associate the same ref designations with the same footprints (Icon that looks like an op amp and a 6 pin dip), make the netlist (Icon sez "Net"), and open that in PCBnew. That allows lots of error checking.

I've never used JCL for assembly (just for boards) but generally for assembly you need to provide something called centroid data, basically X, Y and theta for each part so a pick and place machine knows where and what orientation to put it down.

how-to-generate-the-bom-and-centroid-file-from-kicad

 

Gerbv is a free one.

That's the one I use as well.