Couple of things.
-KSD errors are drive errors. They will clear once the problem with the drive is corrected.
-The small drive boards control the IGBTs. They shouldn't be flickering. If I remember correctly (it's been many months) the boards should always have a solid red LED on.
What I have seen on these that is quite common is that when snapping all of the ribbon cables back in to place, they are put in backwards. This is actually more common than you'd think, as the cables do NOT have an orienting tab on some of them.
Pulled my hair out once troubleshooting a Miconic A that two other techs had worked on a drive problem on before it dawned on me about the ribbon cables.
Good luck.