Well, all of my 12oz bottles are of the same size so there is no need for me to adjust for different bottles. I'm curious if the bottles were a different height by say one inch, wouldn't the capper work at the same setup since the capper "spring ram" is 2-3" in height? My "V" plastic bottle alignment is one piece that has a set bolt to keep it in place. It sounds like your "V" is capable of coming off the stem itself? Weird if that is the case.
I would think with time, you will have an idea of where each index set bolt height should be for each different size bottles you are using. Maybe when you have built up enough bottles of the same kind for a single batch, it will be a lot easier. But if you know what the index should be, it should take less than 30 seconds to move to the desired height.....
You are separating your bottles by height and type before you start capping so that you are capping all the same type at a time, correct?