Hey can you get any more clearer pics? The KYB GR2 shocks are silver colored. It seems like there is still a spring perch there from what I can see. That is most likely the problem.

Here's a question - does the bottom of the skunk2 collar rest on something? The collar is the part that the two disks spin on. It should just be hanging mid air if you removed the spring perches. The inside of the collar (somewhere near the middle) will actually rest on the welds that remain from removing the spring perch. So the bottom of that collar should just be hanging there and you could technically stick something up between the collar and shock from underneath if you wanted to.