I seem to be encountering the same problem. I'm importing a psd file into After Effects as "Composition – Retain layer sizes". If I place one of the psd layers into my main composition, they appear blurry. However, if I choose to place the composition that is generated for the psd file when it is imported in AE, they are crisp (I hope I'm making sense here). I need to have the psd layers as separate elements though, so placing that composition inside my main composition is not an option. Any help would be much appreciated.
The problem with your edges is that a the second layer is positioned on the half pixel. Change the position so the values are whole numbers. If that doesn't work then re-position the artwork in Photoshop.