too bad your bolts didn't come out with the magnet. you may end up pulling the intake to retrieve them, or rent a boroscope and take a good look.
those holes in the head up by the pushrods are just holes for oil drain back and breathing. the intake runners or ports are what you would see if you took the intake manifold off. if you have a stock intake manifold and look at it where it mates to the cylinder head, you will see numbers that designate cylinder numbering. those numbers are cast into the top of an intake runner/port. the oil from the valve train oiling would overfill the valve covers in short order without some drains back to the oil pan. they also make the head lighter so less cost to build. back in the day, guys would deburr the engine block and take all the rough casting slag etc off. then they would coat the interior of the engine with glyptol electric motor paint, like regular paint but made for high heat and sticks like **** to a blanket. anyway, that would allow the engine oil to make it's way back to the oil pan in a hurry so it could get pumped out again with the high volume oil pump.
if you look down one of those holes you will be looking directly at the lifters and the lifter valley. it has drain holes too, but they are more long and narrow. you don't want those bolts to go through the drain holes in the lifter valley because below that is the cam and lifters and then the crankshaft and con rods. lots of stuff to get jammed up in. make sure you account for those bolts. intake gaskets are fairly cheap if you can't find the bolts any other way. can you see anythiong from one of the other holes farther forward or on the head on the other side of the engine? use a good light and a mirror if need be. you could also try the library or online and get a pic of the engine with the intake manifold off so you know what you are dealing with when going in blind.