Unfortunately I mainly have bad news.
TrackMate won't be working well with NaNs. If you sum a number with a NaN, the result is a NaN. So all neighborhood operations will be 'contaminated' by NaNs. This means that almost all spot analyzers and spot detectors will fail. You have to remove the NaNs from the stack, but to do so you have to put a value that makes sense. For instance, replacing it with 0s might not be correct scientifically, depending on how you generate the stack.
Another approach would be to write a Spot analyzer that takes into account NaN and skips them. I refer you to the documentation.
Yes this is possible, but you have to manually edit the TrackMate XML file. Open it in a text editor. The XML file is organized hierarchically be sections, using tabs in in <>. Go to the Settings > ImageData section and edit the filename and folder to point to the image file you want to analyze.
The load this TrackMate file. It should load the image you pointed to. In the last panel of TrackMate, there is an action called Recalculate all features. This will recalculate all features of TrackMate using the new image.
No it is not possible at the time. TrackMate is limited to handling spots that are basically a X, Y, Z coordinates with a radius.