the whiles > while; meanwhile
4 Upon her fell, all naked bare displayed;
all > [as she lay all] displayed > displayed; spread out
5 The sunbeams bright upon her body played 6 (Being through former bathing mollified)
Being > [Her body being] mollified > softened
7 And pierced into her womb, where they embayed
embayed > {Bathed; also: lay or were trapped within a bay (as a ship), were shut in}
8 With so sweet sense and secret power unspied,
so > such sense > {Feeling, sensation; also, perhaps: direction in which motion takes place, hence: intention, purpose (after French sens)}
9 That in her pregnant flesh they shortly fructified.