Katrina,
Your approach is sound. Since they never completed the opt in step, you cannot email them again about this. It's a shame, but they clearly didn't think it was important enough to receive your messages, so it's best not to bug them again.
It makes sense to delete them after 90 days. I would make sure that you don't delete leads that have had other activity in the past 30 days as they may come back to subscribing.
I would also take this approach to increasing CTR.
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make sure you tell them on the TY page to expect an email that has a final step. You could test different messages here to see which ones increase the email CTR.
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See if your deliverability is good on those messages. If they hit spam, that's not helping.
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Make the email really simple and very clear. Subject lines and other text needs to compel them to finish the process. Things like "Confirm your request to receive X" and a follow up that welcomes people. AB test these.