Military basic flight training programs might be of some help in your
research. In addition, the forum folks from Flight Safety, Raytheon,
Simuflight and other contract services may be of some help since I'd
expect that they face the same problem on a regular basis. The only
other resource I can think of are the (mainly European) airlines who've
begun ab initio programs.
All of these sources may be able to offer insight into techniques that
are useful in bridging the knowledge-skill gap you describe. As for the
regulatory-certification issues, I have no clue. The FAA folks who
regularly read this forum would be your best resource.
Pete