Congratulations on the new additions to your family! What cute names!!! Got pictures?
Here is an interesting article on spina bifida/manx syndrome - facts and myths. http://www.manxalotrescue.org/myth.html
Is Roxy's tail 'alive'? I.E., can she move it as a normal cat does? If not, it may be better to have it amputated as that will help to keep her clean and put less strain on her spine.
Is Roxy leaking urine or feces? Or do the feces just get stuck in the area of her rectum that protrudes? Does the rectum protrude all the time or just after a bowel movement? If it is just protruding after she has a bowel movement it could be that the food she is eating isn't exactly right for her. When we had our two spina bifida babies we had to do a good deal of experimentation to get the right food that either didn't cause diarrhea or cause them to be constipated. (both diarrhea and constipation can cause straining and the rectum to protrude). If the rectum is protruding a great deal, Roxy may have a prolapsed rectum which will require minor surgery.
Your vet is right in that you do need to practice very good hygiene to keep bacteria from the rectum from entering the urethra and causing UTI's (urinary tract infections). Our vet was adament (and after two bouts with UTI's we became believers) about giving a DAILY half bath with an antibacterial soap. Once we adhered to his advice, neither had another UTI.
For our babies we just got two plastic dish pans and put them in the sink. One we filled with rinse water, the other we filled with warm water and added the soap. We put KaiWind in the one with the soap -just his back half. He liked to rest his front paws on the edge of the sink and get ear scritches. He sat in the soapy water a few minutes and then we just did a 'butt swish' to make sure all the 'crusties' were removed. Then he was put in the rinse water to get most of the soap off of him. Final rinse was with a spray attachment. Towel dried and then he loved the blow dryer on low to thoroughly dry him and usually a companion or two.
KaiWind wore diapers when he was having family time. There is an excellent section on how to choose the right sized human baby diaper in the archives here. KaiWind had his own room that had easily mopped surfaces for his bed time and when we were at work. You don't want to leave diapers on a cat all the time because cat urine is very acidic and will cause urine scald which is very difficult to clear up once it starts.
I would start Roxy on baths now as a regular daily occurence as it is much easier to control a small kitten than a bigger cat. KaiWind wasn't happy at first either, but in a few weeks he knew that when mommom got home, we'd have our bath and then put on diapers and get to do anything the rest of the kitties were doing.
I'm not sure what you mean about Roxy outgrowing her condition as to me it doesn't really sound like she has that much of a problem. I'd put her on the best food you can afford, give her a good vitamin supplement and see how that affects her feces. If one diet causes very hard stools, then try another food. If that food causes diarrhea, then try another food. As I was saying, it took us several tries to get the right combination for KaiWind. He ate a quality dry food, but all canned foods gave him diarrhea with the exception of nine lives tuna select. Not the best choice, but it worked great for KaiWind.
Hope this helps some. Feel free to ask additional questions and do share pictures of the kids. Does Boston have any issues?