The ports that you are talking about are the Thermactor ports, and they are threaded 5/8x11 UNC.
the link above from Summit is the part you want ($9 ea) , but you are better off buying from Jegs PN 555-51495 (4 pack for $8.99)
The purpose of the ports is to connect the smog pump to the exhaust ports. you can certainly plug them with a regular 5/8 - 11 bolt...but you should put an angle on the tip so that you get a good seat to prevent leaking.
The threaded inserts are 7/16x14 in the inside so that you can attach other accessories to those holes.