I wouldn't return your 50mm based on those focus tests. To have so little light that you needed ISO 1000 at f/1.4 isn't giving the AF system much of a chance, and the depth of field at f/1.4 is wafer thin. Your choice of focus target was also far from ideal. The centre cross focusing point is also quite large (larger than you would presume from the focus point indicator) so areas beyond the focus point indicator may be chosen by the AF system. The 18-200 has considerably more depth of field shot wide open than the 50mm, so if it were off a bit, you probably wouldn't notice it.
Get hold of a proper focus test chart, set it up as instructed in good light and try again. Here is a very good reference for focus testing with a downloadable test chart.
I have the 50mm f/1.4 as well - on one of my D7000 bodies it was a little soft in the centre at f/1.4. An adjustment of -3 was needed to get it perfectly sharp, but I carried out the tuning with a properly set-up test chart in good light. There's no other way to do it properly.