2007 Cobalt SS. Does have an aftermarket short throw shifter. I do not know what kind
The car randomly decides when it wants to have the lower gears (2nd, 4th, and Reverse)
when it decides to not have them the shifter feels like it is further back. Like the upper gears are where neutral would be regularly, and to get it out of those gears I have to bring the shifter way back. Almost as far as it would let me.
I’ve looked a little and it seems like the shift linkage is intact but I’m not sure where to go from there.

 

The issue you are having sound very similar to the issue people have when the roll pin in the linkage to the trans breaks. Pretty much under you fuse box there link that has the shifter cables attached to it. that link is held on the trans by a roll pin that pushed through it. I would check there and see. it can be PITA to get to.