Your error implies that R was not built with --enable-R-shlib or that the setup is having difficulty finding R. Did you also upgrade/reinstall/rebuild R somewhere in this process? At Terminal what is the output of the following commands:
echo $R_HOME
and
ls $R_HOME/lib
Presumably the first shows /Library/Frameworks/R.framework/Resources which matches where the rpy install is looking, but do you have libR.dylib available in the second?
If not, have you tried reinstalling R?