I will summarize as best I can where this stadnds. Maybe it will be of benefit to someone.

I cannot just drop the Qt-4.7.1 directory into /usr/share/Trolltech , as there are all sorts of environment issues that would need to be resolved. I rebuilt Qt version 4.8.2 , and it is there, and it appears to work (at least, it has all teh things you have in the 4.7.1 directory that I downloaded).

Another issue is that after a failed compile of vaa3d, I cannot simply rebuild. Files are moved (mv) so that the second rebuild will fail to find things like the jar files. So I finally realized that I should save a fresh checked out archive before doing the build.

Now, I build with everything "fresh". It appears that the first problem is the following:

=========================================================
qmake -spec macx-g++ vaa3d64.pro " CONFIG+=x86_64"
make -B -j4
=========================================================
./build.macx: line 288: qmake: command not found
make: *** No targets specified and no makefile found.  Stop.
cp: v3d64.app/Contents/Resources/.: No such file or directory
cp: vaa3d64.app/Contents/Info.plist: No such file or directory
cp: ./v3d/vaa3d64.app: No such file or directory
Find released_plugins_more linker folder...
=========================================================
Now build standard vaa3d plugins
=========================================================

5dstackconverter/
===============================
build_plugindemo.sh: line 52: qmake: command not found
make: *** No rule to make target `clean'.  Stop.

ada_threshold/
===============================
build_plugindemo.sh: line 52: qmake: command not found
make: *** No rule to make target `clean'.  Stop.

and then this continues for a long time with all of the plugins.
So we start with
qmake -spec macx-g++ vaa3d64.pro " CONFIG+=x86_64"

Once this fails, there will be no .app file.
There must something in the environment variables or directory structure on my machine that differs from yours.

If you have a compiled vaa3d.app which includes the bioformats plugin, I would love to try it.
If not, I will check occasionally for a new version vaa3d on the web site.
In any case, vaa3d will not build on my machine, and if I have the only mac for which this is true, then I will never solve this problem.

Thank you for the efforts you have made to solve this problem.

--aryeh