I'd cut the bars down if they're still stock length and not think twice about it. I always swap to protaper style bars right away so I've never tried what you're asking with EE guards. I did mount some Acerbis Rally Pros to our 125EXC's stock length bars with no problems, though.
The only thing that comes to mind if you don't want to cut the bars is to mount the inner mount above the x-bar clamps and drill another hole in the guards to fit that location.
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John Brunsgaard - JEB
01 KTM 400 EXC, 99 KTM 250 EXC, 99 KTM 200 EXC, 98 KTM 125 EXC, 98 KTM 380 MXC (gone), 96 KDX 200