So this is what I ended up doing to sort out the problem.
I got the information from this post:
https://community.letsencrypt.org/t/help-with-dns-challenge-and-namecheap/59776/2
I looked into using Lexicon but as it is Linux based and I am running windows machines I thought it would be easier to take a different approach.
Sign up for a free CloudFlare account:
https://www.cloudflare.com/plans/
I removed all DNS records imported by CloudFlare as I didn’t want to use them as my DNS
Set up Certify as per this article:
https://docs.certifytheweb.com/docs/dns-cloudflare.html
Setup all _acme-challenge records on NameCheap as CNAME pointing to CloudFlare nameserver.
eg.
_acme-challenge.mail
_acme-challenge.autodiscover
etc.
I only did _acme-challenge and left all other records on NameCheap as I didn’t want to use CloudFlare as my DNS.
Seems to work so far. I will report back with any problems.
Hopefully this will help other out.