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Picked up motor from the machine shop (LS3), this was a long block rebuild, pre-lubed and smoke tested.
I had read where oil pans have cracked bolting the bell housing on when the pan alignment is off, when I checked it seems to be off slightly. I did put the bell housing on and snugged the bolts ~ 10 ft lbs and it appears fine... I'm just paranoid I guess???
Checked with the machine shop who said that where the bell housing bolts on the passenger side is not close to the area in question and you could not bolt the pan that far off and all is good.
You have nothing to worry about. There's so many bolt holes in the block, covers and oil pan to mess that up. When you center the front and rear covers with bolt holes on the block the bottom of the covers will sit even with the surface of the engine block for the pan installation There's some alignment tools out there to get the covers and seals mounted correctly but I've eyeballed it everytime.
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Oil pan alignment? 
