"I scanned the blueprints for the Flap Ribs (1-6) and got them cutout on a cnc router.  They match the plans perfectly.  They don't match the contour of the flap skins however."

Everyone has had this problem. No rib templates actually fit the airframe, they are usually too small.
With only 900 hrs. to go, you should have realized this a good while ago. I bet your aileron webs were too low also.
Consider the templates a schematic only, cut your ribs considerably larger and don´t cut away for core material initially. Trim your ribs to fit the actual part and you´ll be allright.
I believe prepreg to be the strongest and lightest material for the job, but a LOT of early kits are built with foam ribs and still hold up nicely.

Regards
Tim Jorgensen
360FB  /  55% - only 2500 hrs. to go.............