That same square opening was on my engine when I overhauled it. I just made sure I had a good covering of RTV on the narrow spot that will seal on the gasket. Not a heavy coat mind you, just a good film to be sure it seals. It has not leaked there.
As to the round seals at the rear main, I too would pull the main cap, clean the surfaces and the holes, put a thin film of RTV on the sides and bottom of the cap toward the inside of the crankcase and install it and torque it. Then put a film of RTV on the two round plugs and work them in and out of the holes to spread the sealant around. Push them down all the way into the holes and trim them leaving 1/8" to 3/16" sticking up and quickly put the pan on. If you don't get the pan on within a few minutes the RTV will set up and the plugs may not compress into the holes.
Here is my opinion of the round plug seals. If I build another engine I will not use them. I will just seal the bottom and sides of the main cap and install and torque it. I firmly believe the RTV sealant will stop any oil from getting past the main cap. Be careful to use a very thin coat of sealant on the bottom surface of the cap so as to NOT increase the bearing clearance.