Before I started this ifixit I read a lot of people talking about the antenna not going on properly and problems with the hard drive. I found that the problem is the two grommets inside the front of the casing. These grommets are where the two screws on the existing or upper most (when the case is inverted) hard drive should go into.
I was placing the hard drive flat against the second hard drive I'd added which ment the two screws weren't in the grommets and we instead pushing on the outer casing. This meant the hard drive was in the wrong position and if I had continued with the rest of the reassembly the antenna definitely couldn't have fit correctly. I spotted this and made sure the hard drive was in the grommets, leaving enough room for the power cables to sit between the two hard drives.
With the hard drive sitting correctly you should find everything goes back together very easily. If you get to the end and nothing seems to fit this is probably the reason why!