Appears you may have several minor problems rather than just one but the primary issue, I feel, may be self induced from trying too hard.
Questions: How often do you clean out the coop? What's the weather like? Exactly what modifications to the coop did you make to the factory design (plug holes, seam seal, insulate, etc)? Any chance of a sprinkler system from the yard or or a neighbors reaching the coop? What is your watering plan, is the fount leaking? Any chance a neighbor or child is involved? Are the roof panels tight (possible gapped by the chickens weight on the roost, moving of the coop unit or settling)?
Suggestions: Raise the coop a couple inches for off the ground onto a stable base and re-level for drainage and air circulation, remove the chips, give the coop a through cleaning and kill the mold, drill several small drain holes in the floor or clean out the original ones, remove the caulking and seals you installed to the lower half of the unit, if you prefer lay down a weed mat first to prevent drain holes replugging but switch to COARSE sand or pea gravel for litter. (keep chips in the nests if you want, they sift out easily) Sand is easy to clean and allows drainage instead of absorbing and holding the moisture like chips do which leads to mold when the sun warms the coop. Insure you have good ventilation (never hurts to add more) in the coop because the chickens generated a lot of moisture plus their poo is moist plus condensation on the ceiling from their body heat. Check any inside watering systems for leaks.
Note: Cold chicken feet due to cold sand is not a big issue, if their feet truly get cold they will simply roost and sit on their feet.
Reasoning: As a childs yard playhouse, this was designed to sit out in the rain and snow then drain and dry out to provide a dry, mold free play area for young children. I think you sealed it too much so the water cannot drain as designed and the air cannot circulate to dry the interior plus chips don't drain, they absorb.
I may be full of it but if you would, try this, it may be a cheap fix and may save you a major coop overhaul or loosing birds.