EMC and Drilling

Hello again

Just got a question for all the EMC and CNC Experts.

I want to drill holes at very precise (+/- .002) locations in 3/16"
thick steel locomotive frames. To get the two frames to align to one
another I stack them ( with small screws to hold them together) before I
drill. This makes both sides identical even if I am off a bit. What I
was thinking of was an aluminum tooling plate that I could fasten the
"blanks" too with cap screws. I would align the plate to the ways and
then machine a reference edge (similar to a fence on a wood planer) to
set the frames straigth. Then the cap screws would hold it down. I see
two problems:

1) How do I set the reference position to my part when the fixture can
on hold the part in "Y" and does not control "x". Any ideas?

2) how do I program a drill cycle in EMC.

dave