As for the spheres destroyed in S3 being integral their plans - in Enterprise we saw them transform space with blinding speed.
What speed? It took them some 10 centuries to create the "current"/22nd century Delphic Expanse.
According to my calculations: 1 Sphere created every ~13 years.
Watch 'Zero hour' or 'Countdown'.
The speed of the creation of altered space there was many orders of magnitude faster
than the usual performance of the spheres.
Fast enough to mount the attack in the 26th century, transform an immense area of space in mere years, and be stopped.