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Q: Intake manifold replace, crank attempted, loud clunk now car won't crank. on 2001 Mercury Grand Marquis

No previous problems with cranking or overheating. Found water leaking from crack in thermostat housing.
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Agree with #1, object or coolant in cylinder(s) and possible connecting rod damage NOW. Try to turn engine in both directions with plugs removed.
Did this happen immediately when first cranking engine after the work?
Does that mean a whole new engine? And was it a bad idea to crank the car while the thermostat was out of place?
Whoa! Back up the truck! A cracked thermostat housing will in no way lead to a damaged connecting rod! If the mechanic had the intake manifold removed and now you have an engine knock as well as an engine that won't turn over, your mechanic must have dropped something into the intake port on the head. There is NO CLEARANCE FOR FOREIGN OBJECTS ON TOP OF THE PISTON!! The cylinder head will have to be removed to access the cylinder and remove whatever he dropped in there! And simply cranking the engine will not provide enough force to bend a connecting rod. The mechanic should have covered all ports on the engine while the manifold was removed.
Thank you all for your input, I will be sure to cover all of your points with the mechanic.
T- stat out of place had nothing to do with this! However, google engine damage from hydrolock. Whatever happened, this should have been avoidable!! Did the engine start at all when it was cranked (turned over)? Seems you were there at the time!

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