The very contemplative nature of the hymn upon which this piece is based is the force behind the extremely soft dynamic indications. Reger does not specify the stops, but he does specify that there be two different dynamic levels: pp and ppp, which can accomplished easily by moving between two manuals.
The dynamic indications clearly call for the softest stops or stop combinations on the organ. It is more important in this piece to approach this extreme dynamic subtlety than to achieve clarity. In fact, a very rich, soft string with celeste can be effective on either or both manuals.