这里的“修”应该只限于两人间的缘分，和“灵修”以达到某种精神上的境界并没有太大关系。应该和“修课”的修意思相近，也就是学习、练习，以达到某种状态。

不知道英语有没有类似的成语。

Although 修 plays a key role in the idiom, I think that omitting the verb produces the most natural-sounding result in English. What is lost in omitting the verb is not necessarily restored by a direct translation of it. I would reject "cultivating" out of hand because it sounds too esoteric. Such a verb also demands an object, like "relationship", "friendship", "connection", "bond", or "trust".

If we must translate the verb, consider "forge a bond". I like "forge" because it could be back-translated as 炼, which is proximate to 修 due to the word 修炼. "Bond" is more ambiguous than the other possibilities, but stronger than a mere "connection, and suggestive of fate. A second possibility is "build trust". This is much more specific and explicit, and I like it a lot less, but it may be appropriate if this idiom were being translated for use in a business context.

Even if we were to go with "forge a bond," there remains the problem of how to connect it with the remaining verb clauses, namely 同船渡 and 共枕眠. "To forge a bond (___) to share a boat" - something is missing here. Worthy of? Strong enough? Invention would be required to explicate as there is nothing to translate here.

So I think the solution is to omit the verb (in fact, we also omitted the verbs 渡 and 眠 - no need to specify what one does in a boat or a bed) and let the word "together" do the work. It is not necessary to repeat it in the second clause because "share" is repeated, and it is implicit.
Thus the repetition of 修 is also replaced by the repetition of "share".

Full sentence translation as a poem:
A century's cultivation, together we cross the boat in flow,
A millennium's cultivation, on the same pillow, we find repose.