You have a unique set of issues here, but let's look at the primary one. You have a pregnant cat that, for the most part, won't let you touch her. Things are going to be a little harder for you than with most, but if you are willing to take on the challenge, I think we can work out some sort of equitable compromise between you and your little kitty girl.
You didn't mention how old the female was, but from what you posted, I gather she is less than a year old. You have several options here for the female, but I would suggest that as your first course of action, you get the other one altered right now. As for the girl, if you can lure her into a carrier, you can take her off to your nearest vet or spay clinic and have her spayed immediately or you can allow her to deliver the kittens and then spay her immediately afterwards. Or, and this might not be something you are willing to do, but it is a reasonable alternative for you - you can contact your nearest cat rescue or no-kill shelter and offer to foster this cat in your home if someone who is experienced with semi-feral queens can come by to check on her and assist you. And as an added benefit, they might also be willing to help you place the kittens once they are old enough, usually between 10 to 12 weeks.
Litter size can vary - expect anywhere from 1 to 8 babies. Sorry I couldn't be more helpful with this, but there are a lot of factors involved in determining how many kittens she has and unless you can get her to a vet to be examined, there really is no way to tell until she has them.
As for touching the kittens, you are going to have to be extremely careful with this. Momma cats get very protective of their little ones and if this girl doesn't even let you touch her, then the chances are extremely high that she won't let you touch her babies either. There are many experienced feral cat handlers here on TCS. I might suggest that you check out the Feral and Stray Forum here:http://www.thecatsite.com/forums/forumdisplay.php?f=9
I feel certain there are people there who can help you to learn how to socialize this girl and her babies.
Hope this helps,