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Ahhh ... 300,000 pixels in one dimension is an extraordinarily large image, especially when one considers that the longest pixel dimension of images produced by the largest large format digital scanning backs are around 30kpx, and most are much smaller than this. 

Also, as I recall, the 300k px limit applies to PS, in general, not just it's "Save for web" command.   In addition, the computer memory and processing speed resources needed to process such images will be equally demanding.  Also, since you have said that the images are all slightly different in size, have you considered exactly how you are going to register all the images once they are cut apart, and the time this will take?

All of the above causes me to wonder if there might be some changes that could be made to your overall workflow to improve this process.  Specifically, exactly how do all of the component images wind up on this one, presumably flattened PS file?

Tom M