1. I can't find the ASTNode.Type of LAMBDA in my download of JSBML.
2. Actually, I was looking for a way to take an input string such as "k1 * S1 * 2" such as might be entered into a text field and passing it to a form of the setMath( ) function in order to get it into the FunctionDefinition.
However, in the absence of such a direct method, a workaround might perhaps take the form of code (I've found it in JigCell) that can convert a String such as this into MathML that I could pass to the setFormula(String formula) method.
3. As for working with arguments: I've found that the following code fragment
FormulaCompiler fc = new FormulaCompiler( );
fc.function( fd, (java.util.List) paramList );
where paramList is an ArrayList of ASTNodes of arguments would seem to be able to pass arguments into the function definition. Not sure how this would relate to the body of the formula, though.