This is one case where having the actual reassembly instructions would be helpful. When I put my drive back in the upper position, I thought it was in the right place, even tried to move it and it seemed like it was locked into the holes, but it wasn't, so I had the issue with the antenna plate not going back on. It was so close. It seemed like it should work, but nope.
So, after disassembling again, I played with it some and the best, most surefire way to get it to line up is to hold the unibody upside down when inserting the drive. It has to be essentially at the top to catch the holes. Thin drives make it even more of a problem.
Once I did this, it fit in great and stayed in with no need to hold down, and there was now another 1/8" between the motherboard and the drive, which doesn't seem like much, but in this tight case, its everything. The antenna plate then went in perfectly, all 4 screws were in with no issues at all and the connectors for the two drives stayed on with no issue.