So I now have files with super great astrometry and also proper sky levels. Using those, I DAOphot'd and allstar'd everything, throwing out bad pixels when calculating the psfs. My allstar files ended up having a few thousand stars a piece usually. After that, I prepared everything using DAOmatch and DAOmaster then Allframed it all.
I still don't quite understand how DAOmaster finds the number of stars that it does. For a typical input allstar file of a single exposure on a single chip with a few thousand, DAOMaster finds something like 25,000 stars when looking at all of the exposures on a chip (20 in all). I'm allowing daomaster to use all stars that are found on any one chip, and these numbers indicate to me that there could be double counting as if it makes a list (.mag file) of every star found on every chip regardless of whether it's already been found. But according to the ccdpck_man.doc (guinea pig documentation):
"Finally you specify a match-up radius. After having transformed the stars in frame n to the coordinate system of the master frame, stars will be cross-identified only if their positions agree to within that tolerance.
Furthermore, they will agree only if that is the closest otherwise unassigned star in frame n to that star in the master list, and only if that is the closest otherwise unassigned star in the
master list to that star in frame n. Multiple cross-identifications of the same star in one list to different stars in the other are not allowed.
DAOMASTER will go through all the star lists and match as many
stars as it can to stars appearing in the master list (initially equal to
the list of stars found in frame 1); many of these provisional
cross-identifications will be spurious, but legitimate cross-identifications
will outnumber them."
After allframing, I combine the two bands from a single chip and select out only those stars found in both. The result is a catalog of around 20,000 stars. The files that Ricardo Allframed for me over the summer tend to have something like 12,000 stars in the final catalog file of both bands.
While this is a little troubling, I'm willing to accept particularly because the astrometry was bad before. In creating the final file, stars must match up in both bands. With bad astrometry, it's likely that many of these stars got thrown out. Not all of them did because the astrometry was only about 4 or 5 pixels off, but it's somewhat reasonable that about half were too far off and didn't match up with any other stars so they don't end up in the final catalog. Also, the only files input to DAOmatch and DAOmaster were .als outputs which all contained a sane (few thousand) number of stars, as Ricardo confirmed. So the number of stars are coming from a sane source and I'm using the same parameters as Ricardo did (save for a correction to the transformation relevant to our data set).
2 of the chips are still Allframing. Once they're finished, I'll create the catalog for them and then I'll go about making a master list. With my master list I'll look into making cuts in chi and sharp and then move on to finishing calibrations.