Hi dtowsey,
There is a current limitation in Flow. The run duration of Flow is 30 days. So your flow will time out after 30 days. It might be not possible to send an email reminder 90 days prior to the due date.
Please see more details about the limitation at here:
https://docs.microsoft.com/en-us/flow/limits-and-config
While within 30 days, you may configure the flow likes below.
The function used in the Condition is:
@equals(formatDateTime(items('Apply_to_each')?['End_x0020_time'],'yyyy-MM-dd'), formatDateTime(adddays(utcnow(),30),'yyyy-MM-dd'))
When the End date is equal to today’s date plus 30 days, then send a reminder email.

Hope this could be a reference.
There is also a request on Flow ideas forum for increasing timeout to more than 30 days, please vote the idea at here:
https://powerusers.microsoft.com/t5/Flow-Ideas/Increase-approval-timeout-to-more-than-30-days/idi-p/72202
Best regards,
Mabel Mao