I am sorry,i do not have a hole there.
I do not know what do you mean the stopper might be.
but is that hole even OEM or just made to keep the valve stopped?
I can confirm that the little hole in the picture is not part of the original casting. It was drilled by a previous owner in order to give the metal wire something to hold onto for holding the ceramic EGCV flap open all the time.
OP, you can improvise if you need to to get some other C-Clip and little retaining bolt/mini rod for the EGCV actuator's arm (the big diaphragm part that you are missing) once you can find one. Any turbo rebuild shop should be able to find something off the shelf that will work. Those are the easy little parts to find equivalents for.
I am not sure what size, thread and pitch the three bolts are that hold it on but you can easily find the right type at any decent hardware store. Though it might be understandable not to since taking apart the system means replacing gaskets and without going to the trouble it's around 66lbs or so (I think?) as assembled in your top picture to bring with you into the store. I have a spare USDM EGCV iron housing (minus the important actuator and ceramic EGCV) that I can investigate with to find out though.
Toyota never sold the actuator diaphragm, three bolts, C-Clip and rod bolt or any part of that assembly separately other than the gaskets and ceramic EGCV itself (which has a separate part number but is also discontinued).