Is it a supercharged engine? You will want to check coolant, it should be clean. Remove the oil filler cap and look on the inside of the cap, is there any foam or odd deposits. Check the oil, is it clean and free of foam. The biggest problem for that engine will be LIM gasket failure, and if not supercharged UIM gasket failure. These will both allow coolant in to the engine.
Another thing to look for is rust threw in the rear wheel wells, passenger side is good for this. Check rear seat belts for water staining, also check rear carpet. Both signs of a hole allowing water in to the car. Check the spare tire well for water or signs of water having been there. Signs of a water leak in the trunk.
SAVING THE WORLD ONE BONNEVILLE AT A TIME
1997,1998,2000,2005 year confused Bonneville SSExi. Stock? ish.
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