Your string doesn't have an identifiable pattern, so that means you're going to have to do it by hand.
String.Split
can only help a little.
string str = "AGRICULTURE(FOOD,GRAIN,WHEAT POOLS)AgPro Grain2";
string[] temp = str.Split(')');
temp[0] += ")";
string temp2 = str.Substring(str.Length - 1);
string[3] result = new string("","","");
Array.Copy(temp, 0, result, 0, temp.Length);
result[2] = temp2;
That should give you what you want (may need to be tweaked because I didn't test it).