Thanks to everyone adding in additional advice and personal insight!
I actually was just wanting to relay a bit of stuff I picked up along the way in my own breeding and culturing over the years (started in 1980's).
Yes, the idea of using the dish washer is great, but yours must be better than the one I tried with as I kept getting soap residue on the cups and unless you rinse it out it will get into your media eventually and can spoil a good culture, as for gluing down new media screening.. tissue. If it needs to be replaced awesome but why discard it if all it needs is a little cleaning. The process I laid out only takes about 5-10 minutes to do half a dozen or so cups and lid and with a gently once over the lids and venting material look good as new without tearing.
As for the rest, I have over come the problem with the smaller culture hatch and physical size by simply sterilizing the cups as I explained. What I was referring to with the actual size getting smaller had to do with the mites getting into a culture and it seemed that when the mites got well established (before I started using mouth wash to sterilize the cups before re-using them) the fastest and usually smallest of the fruit flies were the ones that could survive long enough to rebreed.
I rarely experience any issue with my cultures now and I can easily make 6-8 months worth of breeding before I consider buying new stock from a vendor and the vendor's I usually use (one is no longer a 'vendor') selectively screen for mites before culturing, so I hardly ever have a full blown mite problem like I did in the beginning of my frog keeping days... ah to go back and buy lehmanni or histronicus for $25.00... but then again that is why they are nearly extinct in the wild now, so never mind! I just wish I had my frog room from the past and knew then what I know now about keeping and breeding them.
Thanks again everyone and if you have more hints, tips and/or suggestions for keeping our cultures healthy and our animals thriving please don't hesitate