May just be from condensation from the door getting on the floor.
The door should be pretty straight forward. Depending on the model and all, but probably just remove the screws, and cut the caulk around the outside with a box knife. A warm day would probably make it all easier as there is probably a butyl tape seal around the frame.
As for the floor, go past the rotted area a ways and I'd section in a piece of wood with either metal or wood, screwed under the edges of the cut out area to support the new piece of wood and to screw it down to as well. Id then try to fill in the gaps with either your linoleum glue or liquid nails, caulk or something similar on top and bottom of floor. I'd also undercoat the bottom or paint it to help protect it.
Good luck!
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