See [url]Select a PDFset for pythia6 inside Root
Note the two additional ROOT configure options “–enable-pythia6 --with-pythia6-libdir=/your/pythia6/lib/subdirectory”.
BTW. In the “/afs/cern.ch/sw/lcg/external/MCGenerators/pythia6/424.2/x86_64-slc5-gcc43-opt/lib” subdirectory (which you try to use), there exist several different “libpythia6*.so” libraries, but ROOT needs “libPythia6.so”.
P.S. You can inspect the “config.log” file in order to find out why it failed to find your libPythia6 library.