Photomerge (missing manual mode)

We are using photomerge to assemble huge panoramic overviews of the retina. We cannot guarantee an overlap of 30-40% per picture, since we have to keep the exposure of the specimen as low as possible, but it's "easy to assemble" pictures, completely corrected, only a shift in the X/Y Axis has to be performed and the images have to be seamlessly stitched.
Until now we use Photoshop CS2, because it's the last version that we know to have a manual stitching mode (automated stitching epically fails with our pictures). Since the pictures are very big (easilie 12 x 12 pictures of 3k x 3k Pixels) the memory limit on 32-bit forced us to assemble them in patches.
We got a new Core i7 / 8GB Ram workstation now, running Win7 64-bit and installed the trial version of CS5 Photoshop extended to make maximum use of 64-bit... only to come to know that the build in photomerge functions perform even worse in stitching our images and the manual mode is "gone".
I found out that I could install the old Photomerge ( http://forums.adobe.com/message/2242257#2242257 ), but I guess this will be 32-bit and as limited as the one we already use?
Is there any other solution to this? We would like to upgrade to CS5 (for all the other nice functions like 64-bit filters, no more memory limitations, GPU support, etc.) but if it cannot improve the main function we are using.....

The Optional Plug-ins package includes both 32 and 64bit versions of this plug-in as you can see in this technote: http://kb2.adobe.com/cps/828/cpsid_82824.html
You'll also find in that technote a link to the CS5 Optional Plug-ins package.

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