Tiling many aerial photos together

I'd appreciate any advice on this one. I use Photoshop Cs3 to tile aerial photos together. I have done up to a hundred images from an 19 mp camera and Photoshop has done them in one batch in about an hour to 90 minutes. I have a job to do that involves 200 images from a 36 mp camera and it just ain't happening. I try to break the job up by tiling a section together and then doing another section but when I go to put the sections together (or add new photo's to a section)...the large block has been resized so I'm trying to put big images into a small hole. Can anyone help me with this?
[email protected]

Not sure about Photoshop, but perhaps AutoPanoGiga can do it:
http://www.kolor.com/image-stitching-software-autopano-giga-photo-stitching-feature.html
I think the trial version will watermark the output and may expire, but it should be good enough to test for capacity.

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