Tires, wheel bearings, lights, bunks & carpet are good to check but are normal maintenance items. They certainly impact price negotiations. I can't answer to your brake question, but there are plenty of guys here that can and will. Being a freshwater boat should be easy to verify by your inspection. Any pictures?
The hardest part to determine is trailer integrity, as they rust from the inside out. The most valuable tool to test with is a ball peen manner, but the owner isn't likely to let you walk around his trailer whacking away. Knocking with a dead-blow hammer will work, but not as easy to tell, as will rapping on the trailer with your knuckles.
I would suggest you work with a local inboard boat shop (preferably a Mastercraft dealer) to have them go over the boat. Have them do a compression test, and a lead-down test, as this will give you a good picture of the integrity of the engine. Plan to spend a few hundred dollars for this service. It will be well worth it.
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