What should I do with these old cleanouts?
My personal style is to leave them 6" deep with carefully positioned annual flower beds on top of them - give those beds rock walls, if you like, and document the heck out of it.  But if you'd rather extend them to surface:

Those plugs have pipe threads, so a PVC to MPT adapter in the correct size seems the obvious solution to connecting PVC to them. 

I guess annual flower beds may not work so well in the desert - idea being to have a surface feature that maps to the subsurface feature of interest. You need a gazing ball right there, say. This method is subject to loss of documentation and/or memory.

A "hand-hole" would be another approach. Leave the plugs in place and extend access to the surface. You might know them as sprinkler-valve-boxes - a bottomless box with sides and a lid, in plastic or concrete.