Recently I have got a bunch of raw fits images (2048x2048 pixels) of the same sky region without WCS to process in iraf. However, those images are not well-aligned. There would be around 4~5 pixels' deviation for a specific star, thus giving me choppy batch photometry analysis result. Are there any ways to add WCS coordinate using several reference stars or create a user-defined coordinate system so that the same star would have uniform coordinates?
You can use astrometry.net to get the exact WCS of your image.
From the website:
If you have astronomical imaging of the sky with celestial coordinates you do not know—or do not trust—then Astrometry.net is for you
There is a web application where you can just upload your image and it returns accurate calibrations.