Sorry for the bump but this is urgent.

I can tell that you didn't test the sudoers line:
user ALL = NOPASSWD: run-standalone.sh /usr/bin/emelfm2

because it should be :
user ALL = NOPASSWD: /usr/bin/run-standalone.sh /usr/bin/emelfm2

If it doesn't have usr/bin; then sudo is f*****. It will not run any program that needs root (app manager etc) and you cannot edit /etc/sudoers as user

I fixed thanks to "delaroca's" non deb version of plink which connected to my ssh server running on my n800.