Anyone clear up MSD ignition problems by separating the wires going from your MSD box to the your coil from the wires that go to your distributor?

Yes.
MSD is very clear that the magnetic pickup wires going to the distributor should not be run with any other power carrying wires - including but not limited to the coil wires. The pickup wires can be very sensitive to electrical interference and you can end up with a variety of issues - most of which manifest themselves as erratic timing or randomly dropping cylinders. It seems that the newer the MSD unit, the more sensitive they are to noise.

Thanks for the info.

Can I replace the distributor wires with shielded wire and ground one and keep it in the split loom with the other wires? I'm just trying to keep the wires neat.