Hi @rcdrun,
Your domain is being flagged as unsafe by Google Safe Browsing. You can see that here, with their test tool.
Their FAQ has some information that may help. It sounds like once you've solved the problems you can request a rescan through the webmaster tools:
How quickly do you take the site off the list once it’s been cleaned?
Webmasters who have cleaned their sites can request a malware review in Google Webmaster Tools or StopBadware.org. The site will be rescanned and is typically removed from the list within 24 hours if the scan is clean. We periodically check sites on our list to see if they are still infected.
Once the domain is clear from Google Safe Browsing's perspective you shouldn't have any issues creating a Let's Encrypt certificate for the domain.
Hope that helps!