the bb holds the spindle in alignment, so the only answer to your question is "Yes." Misaligned is improper terminology. if the bb fits the cranks and the cranks fit the frame, the proper spindle alignment is whatever it is given proper BB adjustment.

that said, a mm of spindle position is a non-issue. remedy it with tying your shoelaces tighter on on side.

creaking, on the other hand, could be anything. check chain ring bolts first if that wasn't part of the 'crank check.' then check frame. at this point since you have a conversion i'm going with frame. could also be seat post, headset, or hubs. remedy it with a stethescope and a friend and an exhaustive diagnosis and overhaul, or getting new parts or frame.