The best option is to record videos in DosBox and load them into my AutoStitcher program (if you like to use it).
You could probably make a program to press PrintScreen once a second really easily in AutoIt.
Batch cropping is best done in Irfanview. I don't think it can do batch masking; but then, I don't really see how that'd be useful anyway. There must be plenty of programs that do batch "watermarking", and that's the same as masking (overlaying a transparent image).
The program for stitching screenshots together is called MS Paint, or Paint Shop Pro, or Photoshop... or maybe you mean Screenshot Autostitcher. It should be fairly simple to use, you just have to follow the guide on this forum and play with it a bit to get the hang of what the parameters do.