I'm not a Pixinsight user, so I'm afraid I can't speak to the process there. However, I also don't see an obvious alignment issue. If there were such an issue, I'd expect to see doubled stars, star halos, etc. The clear separations in your image between the different emission regions may look like misalignment but is actually a real feature of the Orion Nebula. You'll see the same thing in most other photos of the nebula , including this one I took over the weekend (with much much less integration time than yours):

Yours is larger, has far more detail, and uses a different color palette, but both images seem to show the same basic features, including the clearly delineated emission regions.
The only thing that strikes me is the (to my eye) unusual mapping of your narrowband frequencies to colors in the visual spectrum. For that, I'd second
@Steve Solon and Terry Chatterton's advice--but unfortunately I don't know how to recommend you do it in Pixinsight. (I could tell you how to do it in AstroPixelProcessor...but that doesn't seem like it would do you any good.)