1) the chopped size is really your choice. It is a personal preference issue, not a safety issue, and depends on the texture you want to end up with after opening the jars. Just as with salsas, the bigger your chopped pieces to begin with the chunkier the mix will be when the jars are opened. Some prefer the soupy texture, some don't. So as long as you end up with 16 cups the safety aspect of volume remains the same regardless of the chopped size.

2) I too make them with all sorts of varieties but some require more draining up front. The problem is if you over-drain you end up with an overly dry mix (been there, done that). It is still safe to eat but overly dry, taste is affected, and I worry about effective heat penetration just as with any overly thick product. So the solution I use is to just drain the big juicy varieties briefly and leave most of the juice in the mix. The jars, if overly soupy can be drained after opening just as we do with many canned foods. Better too thin for safety than too thick.

3) the juice or citric acid is a relatively new added safety factor by Ball to several of their recipes. It was added to compensate for just the issues you have asked about - a way to insure safety given the different methods used by different people when making. So in some ways it is sort of optional. If one has the experience to know for sure they have measured accurately and have a good balance of solids and liquid for good heat penetration I suppose they could leave it out. But personally I don't find the citric acid changes the flavor so I add it.

Dave

PS: edit to add I have also made them using bottled lime juice instead of lemon - very nice flavor enhancement.

Thanks as always for your help!