The hole in your 2nd & 3rd pic are for a dipstick tube provision. That's used on other applications that have a front-sump oil pan. Since yours is a rear, it's not used. You should be able to go down to the auto supply and find a press-in metal plug to close that up the right way. I forget the size... just bring the cover to match it up. Looks like a mini freeze plug.
As for the other holes, I believe they are used for the water pump. Double check your block and make sure no bolts are broken off.
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