Did you point the subdomains in Cloudflare DNS configuration to the same IP addresses they were pointing in your previous provider?
What does the error log of your server show when you try to make these requests?
Also, I tried to access lrc.skt.umt.edu.pk - I don’t get a 403, I get a redirection to http://lrc.skt.umt.edu.pk:8000/ - I don’t know how Cloudflare deals with this, but I suggest you’ll run all your services on standard ports (80 for plaintext and 443 for https)…