Sounds like you need to find a better mechanic! I would ask how come they didnt just extract the broken bolts and replace them, maybe at an additional half hour of labor instead of replacing the timing cover. They should have never replaced the timing cover or installed a new timing chain without your consent. Bad situation, I dont know if you have any recourse. You might go and get your old timing cover and have another mechanic extract the broken bolts then tell the original mechanic to put your old cover on and re-install your old timing chain as you never authorized this, and offer to pay the original quoted price for the repair. Another note is the water pump is really easy to get to and broken bolt extraction would also be easy, worst case scenerio he would have just had to take the bolts out of the motor mount and lower the engine a few inches.
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