Photoshop CS3 - Help with Photomerge

I'm doing some work in a lab right now and I'm supposed to put together a large photomerge of a cell (about 220 pictures from an electron microscope). They're big pictures - about 2500 by 2500 each. The problem is that the computer can't handle that many pictures at once, so it crashes.
To avoid this, I made a lot of small photomerges (about 15 pictures each) and started putting them together to make larger photomerges. What happens is that there is a white background behind each of the smaller photomerges and when i put them together, portions of the cell are either faded or completely white. I saw the computer tech do it with CS2, but he's not here today, so I'm not sure about what the problem is. Any help?

Sorry, was looking on other photomerge threads and I forgot to write these -
Model: Mac Pro
Mac OS X - Version 10.5.2
Memory - 16 GB 800 MHz DDR2 FB-DIMM
Free Hard Drive Space - 1770 Gigs? Two HD, one with 840, the other with 930, also an external hard drive with 900 Gigs
The pictures are 6.3 MB each, and there are 220 of them for this particular cell. There wasn't an error message, but the white interference is the problem. The system is new, but the computer tech showed me how to do it on his computer (with CS2) and it worked there.
Thanks!

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