You can just make the cut-out in the tunnel bigger to allow the shifters to move fully, but the best way is to weld-on the extensions the typically come with the kits.
And if you aren't able to weld on extensions, you can get threaded shifter extensions from 4crawler that will work with the threads on the stock shifters.
Edit: Correction, I mis-read, the shifter extensions are for the top of the shifter to make it longer. I don't think it will fix the problem you're worried about.