I had a similar problem: I couldn't run "make" after upgrading to Xcode 4.3. To fix it, I just set my PATH variable to include:
/Applications/Xcode.app/Contents/Developer/usr/bin
/Applications/Xcode.app/Contents/Developer/Tools
Once I had that set up, replacing my old PATH entries referring to /Developer, I could run a "make" from the command line again.
