Here is one scenario. If you had the cuddy open, the boat was in the water, and if the water temperature is below the dewpoint, condensation could occur and collect in the hull. It does not explain the color of the water.
Congratulations ... I am happpy to hear about your success.
Did you take any pictures? I am curious what the assembly looks like in case I need to do a repair. I had a lot of water enter my boat, but I believe it was for other reasons. I described it in the thread, "Tipping Over and Taking In Water" How did only two of you manage lift the boat off the trailer and turn it upside down as well?
ED
I am glad you found your leak, and were able to repair it.
Nope, not everyone has capsized their capri. 10 years owning my capri (no longer an owner), and sailing MANY MANY times... never capsized. However, I have filled the cockpit about a half dozen times!
Also, one thing nobody mentioned here, if you are a mod 1, the DOOR leaks! You are sitting in the water all the time, the door will allow water in.. the angle of the door (plywood you mentioned), is such that rainwater runs across it, while it is in the water. That rainwater has a direct path to the bottommost part of the boat. Sure popping the drain plug allows it out (if you are out of the water say on the trailer).
PS: If you are leaving your boat moored, and you don't already have a motor. Get a trolling motor, and a small deep cycle battery. Also get a small bilge pump and motor. Another choice would be a tarp over the bow half of the boat while it is moored/docked.