If you lived in IL I'd see about putting my spare M1015 in your box "just to compare speeds" and other silly things. ;)
Now that's a true computer friend. Loans you a part for troubleshooting.
I'm in IN. Too bad, that would have been worth a few beers...
PCIe 1.0 should still do 250MB/sec per lane per direction, so an 8x card like the M1015 would be able to move almost 2GB/sec. The card itself though probably has enough latency to affect throughput. Believe it or not but the older cards, when not bottlenecked by PCIe and such, sometimes add enough micro-latency that it adds up to slower total throughput. Of course, in their day it wasn't a limitation because of the speed of hardware at that time, so nobody cared. :p
I have read a few posts about latency you guys discussed. I guess there's no real way to test that. I can't figure out if the individual drive performance is more to do with the HBA or the MSA70, or both. It's connected via 8088 SAS cable (maybe a 3 meter), and then there's the backplane/sas expander inside the MSA70 for the 25 drives. It could be crappy/high latency/all of the above. I have no idea.
At the end of this, I've done all I think I can with current hardware (by putting current 3801E at P16/IT mode), and I've added the 9207-8e to my 'purchase list' for the future. I now understand the chips to drivers relation a little better, and know what firmware I want when I get the new card, and how to check it once installed.
Thanks everyone, your knowledge is appreciated.