But you still haven't told me if there was a fungal mat on top of the tomato gunk. It really is important.
Robert, I don 't know where you read that one should add a cup of water to your fermentation.
All I can share with you is that I've fermented seeds from several thousands of varieties and can perhaps count on one hand the times when I felt it was necessary to add water of ANY amount.And that would occur only when the tomato gunk was too thick. I guess it takes some experience to know that and heaven knows, being the old lady that I am I've had many decades of experience.
I use one pint plastic containers and will sit there and break open fruits and with my hands scoop out ALL of the innards and discard the rest, that firm cell wall, for instance. I keep adding the innards of more of the same kind until the pint container is about 3/4 full.
I never know in advance how many seeds are in there, it doesn't really matter, what does matter is that the fermentaion works. And Not to stir the contents as I think I posted in an earlier post.
Large beefsteaks usually have about 200-300 seeds per fruit, others have less, cherry tomatoes are essentially a bag of seeds so you get lots of seeds from them.
From what you've said I doubt that your fermentation is working, actually I know it wasn't since you got so many seeds that floated,so maybe when you set up the next one you can do it differently to be sure you have that fungal mat and don't add any water at all.
About BER. It is not due to an infectious disease, it's a physiological problem and there are lots of threads here about it. If you are in a situation where you have to use fruits with BER, not a problem. Just cut off the bottom third of the fruits where the BER lesion is and use the rest for fermentaion.
I just went back and re read what you said above about BER and you said it was on the inside of fruits. OK, that's called internal BER and happens from time to time, but is relatively rare, and I could tell you why it occurs, but maybe that's too much info overload. But in the case of internal BER and you HAVE to use fruits that have it, just cut out the black areas and use the rest of the innards to process seeds.
Hope that helps,
Carolyn