If memory serves, Win95's "Boot into DOS mode" takes you to DOS 7.0, which is what Win9x is based on. To have your computer boot to DOS 6.22 you might try just adding the DOS directory right to your C ...
I think it's a combination of non-optimized DOS drivers (few care much about their performance) and your storage drivers. I'm sure your RAID is not delivering on its full rated speed.
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