The pronoun id refers to the event, so you can translate Deo id volente as "when/if/because God wants so/it".
The form id is neuter and thus cannot refer to lapis, and it is accusative (instead of the other morphological option, nominative) because it is the object of velle.
It is not unusual to have other words, especially an object, within an absolute ablative.
The id can be ignored in the English translation if you phrase the sentence suitably.
You could also replace it with sic ("so" rather than "it") or drop it altogether in Latin.
The verb is in the form of an ablative participle, so the (semantic) subject is also ablative.
Whenever you see an ablative of the present participle, it is good to first suspect an absolute ablative and look for an ablative that could function as the subject.
If God wants something, you cannot say *Deus volente — it has to be either a personal form with a normal subject (Deus vult) or an absolute ablative (Deo volente), but mixtures don't work.