Get a new headliner from the wrecker. Get one from a car with a sunroof, it'll already be cut out. Or check the 'For Sale' section here. Some cars are being parted out.
The lights in the doors are on all the time? I'm assuming the switch you used is the headlight switch by turning it until it clicks? With the doors shut?
Check your airbag module under the passenger front seat carpet. It may have corrosion on the connector after all that water.
Wiring diagrams to the level you need would be found on Ebay. You want a 2 or 3 volume factory service manual. There are links to these manuals posted in the 'eBay' section of the forum.
Sunroof switch should be near the map lights above the center rearview mirror.