Thanks to someone mentioning the pedal could be adjusted, I removed trim to check on that, and to my surprise, found that the clutch pedal bracket was completely fractured on the left side, allowing the bracket / pivot to move away from the firewall / master when the pedal was pressed (hope to attach pictures). The metal is pretty thin, but it being Sunday, knew a decent welder and didn't even have to purchase a new one.
When reassembled, it then shifted fine. Travel was not as much as I thought it would be though, 3/8" (9.5mm) but obviously enough. However, there was no way to "adjust" it. It seems on this '06, you get what you get. I guess hydraulic clutches are mostly self adjusting, like brakes?
The picture of the assembly removed- if you look carefully, you can even see the space between the horizontal piece and the vertical member.

 

Wow, I don't remember hearing about that bracket breaking.

Shouldn't need adjustment, because the clutch hydraulic system equalizes when the pedal is up. No adjustment like on older cable clutches.