Stringers are the wooden structural members that run the length of the boat, from the bow to the stern. Bulkheads are the shorter structural members that run perpendicular to the the stringers.
Some places to look for rot: in the ski locker, you should be able to see the stringers that form the sides of the locker. You can drill into the stringers about 1/2" to 3/4", near the hull, to see if the wood is good (light, dry shavings are good; dark/black, wet shavings = rot). On the transom, you may have carpeted panels that cover the transom core. If you do, they should be attached with screws to the wood transom core. Remove the screws, pull the carpeted panels, and you should be able to check the transom. Do the drill test (again, about 3/4" deep with a 1/4" drill bit) and check the shavings. Be sure to check in the vicinity of the where the swim ladder is attached, near the bottom of the transom close to the hull, and around the keyhole where the outdrive sticks out the back of the boat.
The fourth picture you posted (showing the work on the new floor) is a bit concerning because it looks like the stringers were painted, not fiberglassed, which would make me concerned about their ability to hold up when exposed to water/moisture. Check them well!