Here's my understanding of the verse. (Note: I'm only a beginner with Latin.)
Remember (Memento), O founder/maker (conditor) of things (rerum), that (quod) once (olim), you took (sumpserīs) the form (formam) of our (nostri) body (corporis) by being born (nascendo) from (ab) the sanctified (sacratā) womb (alvo) of a virgin (virginis).
Nascendo / gerund vs. gerundive
Nascendo here is a gerund, not a gerundive. That is, it's functioning as a noun, not an adjective modifying some other noun. It's in the ablative case to mean that it's by being born that the Maker takes on human form.
A gerund in Latin is a verb functioning substantively, i.e., as a noun, in an oblique case. In the ablative case, nascendo means by being born. Notice that English has the same construction, also called "gerund", in which a verb plays the role of a noun. "Being born happens early in a person's life." A gerund has the active voice. For example, in:
Desine fata deum flecti sperare precando. [Aeneid, 6.376]
= Stop hoping to bend the will of the gods by praying.
the person doing the praying is Aeneas, i.e., the person being addressed. Since nascor is a deponent verb, nascendo takes an active meaning even though the verb is basically passive (or at least we think of it that way in English: to be born, being born).
The gerundive has the same form as the gerund, but a gerundive is a participle, i.e. a verb functioning as an adjective. For example, in:
Karthago delenda est.
= Carthage must be destroyed.
delenda is an adjective modifying Karthago. It changes case to agree with the noun that it modifies, like this:
Ceterum censeo Karthaginem delendam esse.
= And lastly, I say that Carthage must be destroyed.
Unlike the gerund, the gerundive is passive. Cato isn't recommending that Carthage do some destroying; he's recommending that Carthage be destroyed. In the case of nascendo, though, since nascor is deponent and intransitive, I'm not sure there's any difference in meaning between understanding it actively or passively.
Since there's no noun in the verse for a gerundive nascendo to modify, it seems unlikely that it's meant as a gerundive. It might cause some confusion that in Latin, an adjective can function substantively, and that applies to gerundives, too. For example, mutatis mutandis, "the necessary changes having been made," or literally, "the things that need to be changed, having been changed." Without a noun to modify, the gerundive means "things that are to be X'ed." However, in the verse, I don't think it would make sense to understand nascendo that way; then it would mean "by someone who is to be born".
By the way, I did not think any of the above through when reading the sentence. Happily, even with my fairly meager experience reading Latin, I understood it simply by analogy with sentences like the one above ending in precando.
The text below mentions a couple other possibilities for how to understand nascendo in this context.
Other bits and pieces
I think you are right that nostri corporis modifies formam. Nostri corporis might seem an awfully long distance from the noun that it modifies. In between them there is another genitive, even! Possibly that long distance is actually intentional bracketing of the enclosing clause rather than a compromise with meter. Seen that way, enclosing sacrata ab alvo Virginis nascendo inside nostri corporis formam might even be a way to indicate how the causal relation between the two phrases is intended to be understood.
I think of olim as meaning something similar to English "once upon a time" or "long ago", but not limited to the past, so it can also mean "someday", and not limited to children's stories, so it can also mean "once" or "one time", as in "Once, I adopted a stray cat."
Something I'm not completely sure of is sumpseris. With a short i, sumpserĭs, it's future perfect: "Keep in mind that one day, you will have taken the form…" With a long i, sumpserīs, it's perfect subjunctive: "Remember that once, you took the form…" I figure that the past tense makes more sense here, but the subjunctive mood seems strange because the event is already accomplished fact. Possibly imperative memini customarily governs a subjunctive verb even when referring to known fact; someone with better knowledge of Latin will have to clarify that. (See new question about this.)
Alas, I'm pretty sure that vowel quantity plays no role in medieval rhyme, so I don't think that we can use the short vowels of corporĭs and virginĭs to infer the quantity of the last vowel in sumpseris.
Regarding gerund vs. gerundive, perhaps one could argue that nascendo modifies an implied noun te, so the meaning is "by you who are to be born". I don't think this makes sense with either reading of sumpseris, though. As sumpserĭs: "Remember that thou took'st human form by thee who art to be born…" As sumpserīs: "Keep in mind that thou wilt have taken human form by thee who art to be born…"
Ablative of time?
I found a few English translations that treat nascendo as referring not to the means but the time of the Maker's taking human form. The Manual of Devout Prayers (1688), p. 84, has:
Divine Creator, bear in mind,
That thou, of our corporeal kind,
The form assumedst heretofore,
When thee a Sacred Virgin bore.
Unless nascendo is commonly used to refer to when someone was born, analogous to "et requievit die septimo", I think it needs a preposition or adverb to refer only to the time of the birth, but I thought I should mention this. The grammar might mark an important point of theology: that the Maker got human form from Mary's womb, indicated by ab. I think that in ordinary Latin grammar, this means that the act that transferred the form was the birth—hence the need for an ablative gerund.