You're braver than I am. My late grandfather's last pair of Bostons were classic littermate syndrome dogs. Couldn't be more than a couple feet apart, almost impossible to do any kind of individual training with (well, he didn't exactly try either, but not my dogs). Worse, the male was pushy and more confident and made sure he got most of everything - attention, pets, food, beds, toys... this is another dynamic can happen with this situation, where one pup becomes a bully who steamrolls the other so that the less confident dog winds up withdrawn and disengaged, even if they also can't function when they're separated. It never bothered my grandparents, exactly, but their expectations for their dogs ended pretty much at "housebroken" and "will kind of go to their room when asked, sometimes". It's hard to believe it was best for the dogs themselves, though. I was worried my grandmother would wind up with an anxious mess that she couldn't handle when the male had to be put down (old age problems - they outlived my grandfather), but the female does seem to have adjusted and is enjoying being the only dog for once.
Not sure if that experience is helpful, but I hope it's a little informative at least, especially with the pushy/bully behavior you want to watch out for. I wish you all the luck, you're undertaking no small thing here! And you clearly care and are willing to put the effort in, so that counts for a lot.
For the water, you can try no-spill/no-splash bowls, sometimes marketed for travel (eg something you can use in a moving car with less risk of making a mess). They have a lip around the rim that leaves a hole only big enough for a muzzle, so maybe less tempting. Other tricks are using hanging bowl/bucket attached to a crate so that their water is off the floor (works for some dogs, but others may just find it a challenge), and there's even drip water bottles - the kind you see for rodents and rabbits - that are dog-sized, again for hanging on a crate or pen. I've never used them and I'd want to monitor very closely if you do try one to make sure your pup understands how it works and is actually drinking well from it, since they're less intuitive for dogs than a bowl. There's also silicone/rubber mats meant for catching spills you can put under the water bowl to at least attempt to contain the mess.