Hi Maverick,
OK, I did the same except I didn't do a clean install, I cloned from my pre-existing OSX 10.9.5 Raid 0 disk array (in normal drive bays). This sort of thing has always worked well for me in the past, and I'm not sure how I'd consider that a likely culprit (it would be a pain to redo it at this point, too).
Can you confirm that in your 3,1 you were getting ~800 on BM?
Thanks.