Which is better and more greatly rewarded: prolonging the standing to recite a thousand verses in the night prayer, or prolonging the bowing and prostration and all other pillars, knowing that prolonging the latter might prevent completing the thousand verses?

It is better to follow the Sunnah of the Prophet, peace and blessings be upon him, in the manner of his prayer. He used to pray with a balanced approach, equalizing between its pillars, so he would lengthen the bowing and prostration if he lengthened the standing. Whatever is more beneficial for the heart and more conducive to its humility is more deserving.