The files are as follows: 

image.gif                    Picture of overall PCB, with a 25mil grid. 
oe_coptop.grb/ps/pdf         Top copper layer
oe_copbot.grb/ps/pdf         Bottom copper layer
oe_soldermask.grb/ps/pdf     Solder Mask (same, both sides)
oe_componentsilk.grb/ps/pdf  Silk-Screen Layer, Top Side Only.
oe_plated-drill.grb          Drill file
opt-enc.pcb                  Design in .pcb format
                             (http://bach.ece.jhu.edu/~haceaton/pcb/)

For alignment purposes, we've included the same set of files with the
addition of a 2mil border around the PCB. These have the same
filenames as the above, only oe_ol instead of oe at the beginning.

Drill holes for mounting should be a close-fit for a #4 machine screw,
so 0.116" diameter. That exact size is given in the drill files. A
technician on your end said your equipment would automatically adjust
the drill size to account for plating. You fabbed a previous version
of the board before, and this was correct size. 

The overall PCB is 1.3" tall and 2.3" wide. The only important
alignment is with the top of the PCB -- the PCB is an optical encoder,
and if there is additional spacing above the top, it will come in
contact with a moving object -- the top, however, can be cut
arbitrarily smaller from what is specified, so long as it does not cut
into the silk-screen layer, pads, or traces. However, this tolarance
is not tight -- the 0.010" listed in your FAQ is more than
enough. Otherwise, alignment is not critical -- on the sides, it just
needs adequate spacing so that the PCB can be screwed down without
breaking, and on the bottom, the only limit is the silk-screen text
(although we would prefer to cut as close to the silk screen text as
possible).
