I shot a hyperlapse last year, but there was some serious light shifts happening and the foreground was going from bright sunny to no sun at all in a matter of minutes. I tried to play with lrtimelapse yesterday to fix this but didn't have any luck.

Is this clip garbage or can it be salvaged?

https://vimeo.com/124884871

It's not that bad, I think some problems are due to the clouds coming in and casting shadows then going away again. Try not to overdo the editing in Lightroom, since lightroom will apply some settings based on the content of the image - this might introduce even more flicker. Then use Deflicker in LRT, make sure to set the reference area to an area that makes sense, check my Deflicker Tutorial if in doubt.