Well done you. I always worry when disconnecting the fan connector as the leads are quite fiddley. I also find that standing the Mini on its side is the only way to ensure that the lower bay drive is securely seated in the edge support holes (not in the manual).
I was definitely really nervous about things not lining up properly. Like the instructions said something about a guide on the back of the power supply and make sure it lines up. I really had no idea what it was talking about so just hoped for the best.
It was pretty much the same with the drive. It said to line it up and it just kinda slid in and wasn't moving side to side so I figured it was in. All of the screw holes lined up perfectly with the antenna plate as well. I think that when you are putting the second drive in, it is a lot easier to line up since you have the other drive to guide it properly.