Hmm, I understand.
For our translation project, I had coded a re-paker (command line tool in python) to create the monkey.pak file from all the extracted (and modified) files, so, that would probably have helped you with the lordtrilobite's dxt issue.
It would require more steps than if you had lordtrilobite's dds files, but it should work.
So basically the steps to get the modified dds to work on would be:
1) Extract all files from the original pak file using bgbennyboy's MISE Explorer 0.5
2) copy any modified files overwriting the originals
3) repack the files into a new pak
4) Extract the modified dds you need again with bgbennyboy's MISE Explorer
I know that you have now probably finished your work, so that's no more of use to you, but pm me if you are interested in such a repaker. (it only works for SoMI:SE at the moment, not MI2:SE).