With regard to the maximum Z slice, the limiting factor in the biorad is
actually the size of the PMT photocathode.  Because of the long detection
path length design, the PMT size acts as a significant "pinhole".  Since
the maximum aperture is 7 mm and the PMT photcathode diameter is 23 mm,
you could get a tripling in Z depth by completely removing the aperture.
However, there may be some limitation due to the holes in the second filter
block holder.  The other problem with laser scanning imaging with an open
pinhole is that you are imaging an hourglass shaped illumination instead of
an ellipsiodal one.  This could be avoided by slightly underfilling the
back aperture (this is easier said than done) to produce a larger
illumination spot.  Anyway the maximum Z section that you would expect
for the biorad (pinhole open) and a high NA lens (40X 1.3 NA) would be
about 3 microns.
 
The eyepiece does cause the overfilling of the back aperture.  This is
necessary for diffraction limited focusing.  You must keep in mind that the
objective lens acts as physical transform: angles in the back aperture
correspond to position in the image plane and vice versa.  The scanning
is stationary in the back aperture, only the angle varies.  This is needed
to assure uniform illumination over all parts of the field.
 
                                Dave Piston
                                Vanderbilt University