1. I wrote a script several years ago that will automatically stack fits images. MaxIm was kind enough to put it up on their web site. You can find it at http://www.cyanogen.com/maxim_extras.php  Go down to "Free Plug-ins, Add-ons, and Scripts". The third script down is StackFitsImages.VBS. This will do what you want so long as your images are FITS format (and they should be if at all possibel). Just follow the directions. Especially the part about not having any images in your folder except the ones you want stacked. If you have your Aunt Matilda's clam chouder recipe in the folder, it will try to stack it.
2) I use average or median. There is no difference between sum and average except for a scaling factor. I stay away from the more exotic (and potentially nonlinear) methods.
3. Trying to load 300 images into memory with MaxIm is tough. Things get pretty slow and eventually you run out of memory (depending on the size of your images of course). MaxIm has a batch calibration tool that works very well. Go to Help > Index > Batch Process. I'm not sure how it handles format changes. Are you sure you want to use IEEE format? Fits is the standard format for science and we should stick to it if possible.