Hey Ani -
I have the same rig, Mixpre > MR1000, and have the exact same issues. The signal coming out of the MiPre is very hot, and it seems just breathing on the dials puts the output too hot for the Korg. The Korg's preamps can't handle a lot of juice, so clipping them is very easy (I have the same issue with my Senn 8040s). The specs for the MR1000 say TRS balanced tops out at +4dBu, unbalanced at -6dBv.
I've tried two solutions:
1) put -10db barrel attenuators between the MixPre and the MR100. This has worked reasonably well for me
2) use the tape return - there is an output from the MixPre that takes a stereo 3.5mm male. Get a connector that goes 1x stereo 3.5 mm male to 2x mono 1/4" mm male, plug the stereo into the MixPre and the 2x monos into the Korg. I also do that with my Korg MR1. The sound comes across pretty good.
Good luck!
Mike