A couple of things that I see.
The flange on the header is too thin. A good quality header will have a flange the same thickness as the intake manifold flange.
The other thing I see is hardware. The nuts, bolts, studs, washers are all wrong. The OEM washers are the best option, especially for the studs that share the intake manifold and the header. Some of the ones I can see aren’t even clamping the header, and are doing a poor job of clamping the intake manifold. The stackup of flat washers isn't transferring enough clamping force through both parts to the head.
One area where I diverge from stock hardware is I use brass nuts, made for exhaust assemblies. And I use high temp antisieze on all the threads so it will come apart when it is time to do so.
As for the gasket orientation, I don't know if there is a right or a wrong way. I would think the side with the widest bit of steel around the openings would be better next to the head, as that is the first stop for the hot exhaust on its way out of the engine.
I don't know if a copper gasket is available for the L series engines, or if it would work to seal the intake manifold side. But I had a Chevy 454 in a pickup that I used to tow the race car with that kept eating exhaust manifold (and header, I tried both) gaskets. I finally fixed it permanently with copper gaskets.
Here is a picture of the setup I use. I use studs for all the fasteners except the six along the top that are only common to the intake manifold, which are Allen head with a lock washer. The OEM washers are for all the studs that share the clamping loads between the intake manifold and the header. The three studs that are only common to the header get a grade 8 flatwasher (get a high quality washer for this, that has a close fit to the stud, and is thick - a business that sells fastening hardware as their primary product is a great place to get all this stuff, not Lowes or Home Depot, even the chain auto parts stores suck).
Get good hardware and a better quality header and you should be able to get the leaks fixed.
Also, it takes me several different wrenches and an Allen socket to tighten all the nuts and bolts for the intake and exhaust.