I've noticed the same thing on my SC2400, not much ground clearance under some implements when they are raised. I decided against a shorter top link though after using the box blade. When doing the final passes with the box blade I had the top link all the way out. A shorter top link wouldn't have worked for this.
I think that the problem has nothing to do with the top link. I think that the problem is that the machine is a SUB compact and sits low to the ground. I have noticed a huge difference when using implements designed specifically for sub compacts machines, like the XB line from King Kutter. If your blade is meant for a CUT and not a SCUT, there's not really much that will help.
Of course, even with the XB implements there are still limitations. Take the middle buster for example. In order to have any usable depth to the cut, there is a limit to the height it will raise up. We have a lot of hills, and the only way to transport the middle buster without scraping the ground is to either take off the blade in for transit or just carry the whole works in the FEL until I get to the garden.
I've got an XB 5' blade, and it sits plenty high for transport in the center position. If I angle it all the way though, the bottom corner catches on even a slight incline.
All that being said, I love how low the machine sits for two main reasons. 1) My knees would scream constantly climbing into anything larger, and 2) The lower height means more stability on all of our hills and slopes.