You haven't provided an example of something with a W in it so that is untested. I think this will solve your problems:
YourList = {"(GPN) CI-4/E7/DH-1 15S-40 L1807", "DEO (GPN) JD CI-4/E7/DH-1 5S-40 L1807", "(GPN) JD CI-4/E7/DH-1 40 L1807"};
Part1 = Part2 = {};
For(i=1,i<=N items(YourList),i++,
SubWords = Words(YourList[i], " ");
For(k=1,k<=N Items(SubWords),k++,
If(contains(SubWords[k],"S")>0,
Part1[i] = SubWords[k];
k=N Items(SubWords)+1;
)
);
);
For(i=1,i<=N items(Part1),i++,
If(contains(part1[i],"W")==0,
Part2[i] = right(part1[i],2);
)
);