I thought stripping an IDE cable would be really hard until I tried one the other day. IT IS EASY! You can strip the end with a utility knife, and the wires peel apart to give you 40 separate wires going to the IDE connector. As long as the IDE cable wires are long enough to reach your controls, you don't need to use a block.
Also, instead of trying to crimp quick disconnects onto the small wires, use a small solder joint. This is actually very fast (I wouldn't have thought so) and if you were willing to solder 40 wires to a PCB so close together, then 40 solder joints connecting easily separatable wires to disconnects should be a snap for you.