Update: 2nd a 4th were doing the same this morning on the ride in. And 4th was working fine on the ride home but it absolutely will not up or downshift into second when moving. It will start in 2nd with absolutely no problem. When your not moving you can distinctly feel it going into every gear. When you go for second moving it feels like it’s not going all the way in no matter how hard you push it and throws the shifter back in neutral as you can see in the videos.

Here is a video of when it wouldn’t go into 2nd or 4th this morning 2nd it pops out and I just go to 3rd than 4th it popped out than I show what happens if you try to hold it in (grinding)
Than a video of it starting in 2nd no problem:

 

Seems the two rearward positions 2nd and 4th aren’t reaching their positions, I suggest you replace the bushing as it’s easier and less expensive then shift cables.

 

The link you shared for the bushing is listed for an automatic. Is it the same bushing for a manual?

 

I suggest you contact them to confirm, I searched manual shift control

 

You need to fix your cable problem or it will never shift right.

 

May we assume the clutch has been definitively ruled out?

 

I found this old thread with pretty much the exact same issue… https://www.chevyhhr.net/forums/driv...-manual-59445/

 

Clutch was replaced around 25,000 miles ago. As well as half shafts more recently

 

I might just order cables and find the actual issue as I replace them.

 

I was actually thinking more like the hydraulics or the pedal. If it doesn't disengage completely downshifting becomes difficult. There is a history of the firewall wearing out where the pedal mounts; which would keep the pedal from full travel. Or the hydraulics are messed up.