If the glass has turned brown or is soggy you could have serious lamination damage. Check all of the lids and seats for tears, cracks, and hinge condition. One tip never buy a used boat in the rain. In the rain many finish problems are hidden when the boat is wet. Walk on the floors and decks.
Soft spots mean big trouble and a very expensive repair.
Now its time to check the transom. First look for stress cracks in the transom. If they are there its not necessarily more than a cosmetic problem. What you want to do is trim the motor up and put your weight on it. If those cracks widen or you get any flex in the transom just walk away.