Sorry, I haven't been on the boards the last couple of days.....
The first thing I'd recommend for your dogs is a thorough physical examination and blood work including a urinalysis. This will help you rule out any sort of phyical abnormality that might be contributing to the problem....
That said, unfortunately from the description you've given, I'd be much happier to find a physical problem than what I'm suspicious might be going on---some behavior difficulties.
You mentioned a prior history of separation anxiety with the shepard. Separation anxiety is just like OCD in a human in many respects with dogs. The dogs don't "get over it"---although we'd like to think that they do. They develop/learn/are medicated into coping mechanisms that allow them to live a normal life without disruption or as normal of a life they can have without disruption. You mentioned children and housework. Those are a recipe to send an otherwise anxious dog over the edge. And unfortunately, German shepard mixes seem to be highly represented in dogs with just that sort of predisposition. You didn't mention age of the children, but if they are young kids, remember they will change as they age---for some older dogs, yelling, crying, pooping kids can be very, very stressful. Combine that with loud saws, hammering, and other construction noises and with bad smells of painting and you might have had enough to push both of the dogs over the edge.
You didn't mention if the male dog was intact or not, but I'm going to assume from the "leg hiking" that you described that he is. Urinating on the floor can be an early sign of prostate enlargement or prostatitis. That can be determined by a Physical and urinalysis. It can also be a territorial issue brought on by environmental stress.
The other thing you really, really need to determine is is this a male dog that has been pissing in your house for some time or is this a new development. The longer its beeing going on, the more of a problem it may be to fix. I had this type of a problem with my own dogs. My aunt came to visit with her little nonhousebroken pieces of crap, who proceeded to piss all over my upstairs bedroom. This set off my lab, who then took months to get him to quit sneaking into that room and squirting a few drips on the edge of the bed.
The bottom line is get a physical and laboratory work done first, then work on the problem from there.