If it were me, and my vet had experience spaying and neutering pd's, then I would probably have it done. In my own experience right now, my vet has never spayed a pd, so I chose not to have my girls done. There are health benefits (and some behavior benefits) to spaying and neutering, but with an inexperienced vet, I decided it wasn't worth the risk for me. I'm not trying to discourage spaying and neutering, mind you, that is my choice in my own situation.
I have heard about pd's ripping out stitches too. That was another reason why I chose not to have it done. If the vet is able to wrap them properly with a "vest" type wrap, they shouldn't be able to bend down to get at the stitches. There is a book called Bringing a Prairie Dog Into Your Home that shows how to properly use the vest type wrap.
Regardless if you have them done one at a time or all at the same time, it's a good idea to keep them separated. Pd's like to groom each other and they might pick and chew at each other's stitches.
As far as sexing goes, I think there is a bigger spacing between the anus and the urethra on males. I'm assuming you have looked at all three and noticed that Biscuit looks different there?
As far as breeding, I have read that it is very difficult to breed pd's in captivity. I have only heard of a handful of people successfully breeding pd's in captivity. They need the right environment (lighting, temperature, housing) to breed and have babies. I honestly don't know if your males would pick on your female during rut if you don't have them spayed. Someone with more experience with housing unfixed males and females together will have to answer that question for you.
You need to start cutting back on the puppy food
as they get closer to one year old. I think that they should be switched to a less fattening food like Fit and Trim. That was recommended to me from the person I got my pups from, who gets them directly from Lynda Watson (and wrote the above mentioned book with Lynda Watson and Betsy Callis). Pd's can become very obese easily which can cause other health problems. They should have lots of Timothy hay, pd pellets, and water as their main diet. You can give them little treats sparingly.
I think you're always going to have to deal with temper tantrums.
They are just like a 2 year old being told to stop playing and go to bed. I think everyone has had to deal with a pd getting angry when it's time to go back to the cage. I try to trick mine. When they are playing, I will pick them up, pet them, whatever. If they behave themselves, I put them back down to play some more. If they start chittering, it's back to the cage! My one pd got to the point that she knew if she behaved, she got to play more. If they behave but I still need to put them back in the cage, I'll give them a treat for good behaviour.
Chewing and digging is natural for them. You can try telling them NO when they dig and chew the carpet, or you can try redirecting their attention to something else. Anytime a pd is out of their cage they should be closely supervised. They can get into all kinds of trouble, not to mention they don't know that they shouldn't be chewing on certain things....like electrical cords.
These are just a few suggestions for ya. I'm sure other members here will join in and share their knowledge and suggestions with you too.
Don't be afraid to ask questions! That's what this forum is for!