For the contamination problems, I would completely disassemble and clean the lines from keg to tap, including all of the faucets. Nuke them with PBW. Then put it all back together. I keep a spray bottle of starsan next to my taps and normally spray up into the faucet (perlicks) after each beer, because I can't always be sure I'll be back for another beer that night. The little bit of residue left could be a place for bugs to grow, and from there they can get in your lines.
For the carbonation/foaming problems, your lines sound too short to me. They give you the rating for the hose in terms of psi lost per foot based on friction, but I've found I need more length to reduce it down enough to give me a good pour. Start with something like 6 feet and see how it goes, and cut it down a few inches at a time until you get the pour you like. It's kind of a pain, but once you do it for one the others should all be the same.
For the saison, yeah, if you're pushing it with 12 psi it will get flatter as you go. If you're using a splitter to push from multiple kegs, you could take the other kegs off and push it up to 24 psi again for a few days to recarbonate it, but then you'll need to blow off pressure again to serve at 12 psi or it will come out too fast, unless you swap out the hose, but then it will be too slow as the pressure in the keg drops. It's a total pain, but I've done that juggling act. I just got a 5-way secondary regulator though, so now I can push my kegs at different pressures. The cost hurt, but I'm going to be happy with the flexibility.