Not sure John... a couple of things though:
The lib and include paths in the generated command are three levels up "../../../lib" but you specified "../lib" in your config. Be sure to name your .user file Makefile.user (capital M). Not sure why else it would be wrong...
Your AQ libs actually appear to be at just ".." like in the default Makefile setting. And the CW install folder has its own "lib" folder. So something is off there. Try not changing the default AQLIB_PATH.
Haven't tried CW 3.0 -- they might have changed directory structure or who knows what. Is 2.x still available?
STM32F40_41xxx.vec is the file you need in STM32 folder. Not your problem yet, but it will be.
-Max