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That bolt goes into the head, so it would sound like the head has a stripped hole unless it just wasn't torqued down (same bolt on mine loosened up after a few heat cycles when motor was rebuilt). It's right next to the #2 intake port, so you could develop/have a slight intake leak at the gasket below. I would suggest fixing it right too.
As for the alternator, I don't think it's possible to misalign it. Several people remove that rear bracket altogether with no issues. Anything drawing on the battery with key off? My qtp dpdt switch had an LED light that would kill the battery in a week.
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1997 Camaro Z28 - 355 LT1, T56, CC503, LTs, ORY, Bald Eagle-back exhaust, !emissions, Lingenfelter CAI, EWP, !CAGS, BMR LCAs, UMI PHB, Koni Str.t/Koni SA, C5 Z06 front / LS1 F-body rear brake swap, factory hurst with short stick 
2014 2LT Cruze 2.0 Turbo Diesel
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