I understand that given the danger to your kitties it is not safe for them to come and go as they wish.
Of course that is extremely difficult for them to understand.
Cats that are used to being outdoors as they wish tend to enjoy getting exercise and all the stimulating sights, smells and sounds that go along with the outdoors.
While we cannot fully replicate all of that perhaps giving them more to do inside and increasing stimulation will help get them happier.
Encouraging play behavior and exercise is a natural way to relieve stress.
Fishing line toys and mechanical mice for them to chase could help satisfy their need to "hunt" prey.
I also recommend hiding treats for them to "hunt down" in cat trees or kitty condos. If you can find one or a few of these with several levels and lots of hiding spots and perches to climb on and sleep may make them much happier. Putting one near a window so they can at least see outside may help too.
Perhaps building an outdoor fully screened in enclosure off an upstairs window, or on an upstairs patio or porch so they can go out safely, but cannot be reached by people outside, is an option.
If part of their stress seems to be that they aren't thrilled with using a litter box you can give them more than one option for places to eliminate. I recommend you using one more litter box than the number of cats so there is no litter box guarding and make sure all boxes are very clean. That means scooping stool twice daily (as you probably already are) but also a complete litter change weekly. Are your litter boxes covered? Many cats don't like covered boxes. Put the boxes in different places as some cats like to defecate in a different place than they urinate. Some cats prefer a different substrate to poop and urinate. Make sure they have privacy and can't be interrupted mid bathroom break. You may want to try unscented plain clay litter or clumping litter as that is what many cats seem to prefer. Some outdoor cats like potting soil or sand as a litter option. These are messy so you may need to put matts around the boxes that have those substrates. Finally if they are large fellows they may simply need a roomier box. I find the large, very low sided, plastic containers that slide under things for storage work well in those cases.
I recommend you continue Feliway too as a stress reliever. You can also use a homeopathic called Rescue Remedy drops along with Feliway. This is added to their food or water and may help relieve some stress.
Zylkene is another supplement that may help relieve their stress. Here is a link if you'd like to read more about it: http://vetoquinolusa.com/Products/Behavior/index.html
In short try to increase play time, exercise and stimulation, give them more options to eliminate and perhaps add a calming supplement to help them adjust.
My best to your kitties, I am sorry that they are paying the price for human cruelty.
Please let me know if you have any further questions.