Auto focusing cameras are wonderful. The downside to AF is that whatever manual focusing skills we have acquired over time, tend to disappear instantly. This coupled with the viewfinders on today's cameras - which are not optimized for manual focusing, results in what you are seeing. I still have this Spotmatic II from 1970 and its viewfinder is wonderful. Switching to my K20, is difficult for me to manual focus, I have found. A katzeye would certainly help. This is something that I have not gone to yet, as I tend to do landscapes, and use hyperfocal focusing more towards the infinity end, so it becomes less important.
For what you are trying to do, I think the results are pretty good. As everyone else has indicated, a tripod, 2 second mirror up, external shutter release, live view to focus, etc. will certainly help.
Also, 85mm at say 3 feet, @ f2.8 only gives you a dof of 1/2 an inch.
That is pretty thin for the object you are shooting, so by design - most of the image will be out of focus anyway, and you are at ISO 1600. So, either a lot more light, or some mechanical stabilization is in order.
Edit - Also for best resolution I would tend to guess that f4 to f8 will provide the best for this lens. Someone probably has done a review on this that provides a resolution histogram by f stop showing center, edge and corner. The more you stop down to gain resolution, the more light you are going to need (or the longer the shutter duration will be required). Also, to reduce noise, and to help with resolution a lower ISO will certainly help (ISO 200) but that will require even more light or slower shutter - which again pushes you to mechanical support....