Great idea with mason jars. Plastic containers are flimsy and not reusable. I usually just freeze my fruit flies to control their population.
Plastic Deli Cups are actually re-useable with the freezing method but is a bit flimsy(at least the current stock at Josh's frog) and if not careful you may end up bending and breaking some. It's really easy to clean, just use a plastic spoon to scrape off the old pupae on the walls, then rinse.
I'm thinking if using the wide mouth mason jars, you can use the same freeze method and just pull out the frozen old media/culture with a bit of nudging.
Josh's frog updated instructions is to just pour boiling water and not mix the media. I've found it works better when doing that keep the media from getting as wet. I've found using the fully plastic and not cloth vented lids, where I live, the media gets too wet towards the second/third hatch of the culture and the adult flies drown in the wet top part of the media. As mentioned before the plastic vented lids keeps the culture more humid. It's better if I don't mix the media and this method also worked great with my home made media(it's still producing great at 6 weeks), although you should probably be throwing it out by this time to prevent mites/mold that may take hold easier on the end of the culture. Josh's frog has powdered honey in their mix, so it's more wet compared to my home made media with out as honey is a natural humectant, all things being equal.
Now I'm adding coffee filter stuffed with some excelsior and hopefully it can control the humidty for Josh's frog media, as someone tried the coffee filter + excelsior and they've had great results with it. Although my home made media is working great, I probably don't need to worry about media being too wet, the coffee filter is extra surface area and allows me to put less excelsior. I find if you can keep the top part of the culture from getting too wet or dry it produces longer.
Now you don't need to min/max your production with these little tweaks as culturing is really easy and is forgiving but I'm a bit weird like that and thought I would share.