Make sure that all your critical files are reorganized. One thing that affected us hard in the past was the fact that we never ran a MAPICS Reorg in ages. Files were so big that it was not part of their periodic tasks. Once these guys are reorg, you might feel the improvement in the system.
You can refresh a test environment with the production one, run the two MRP runs in it, then do a MAPICS Reorg (or maybe you can explore the possibility of only using the RGZPFM on each of the files with deleted records) and then run two additional MRP Full runs and then compare the times.
My theory is that you may have an improvement in time.
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