OMSA self signed certificate - CLI generation and assignment of the self-signed certificate?

So I scanned one of my boxes with Nessus & it returns the following:

1. SSL Certificate Cannot Be Trusted
2. SSL Self-Signed Certificate
3. SL RC4 Cipher Suites Supported
4. SSL Medium Strength Cipher Suites Supported
5. SSL Weak Cipher Suites Supported
6. SL Certificate Chain Contains RSA Keys Less Than 2048 bits

So I went to them OMSA page & changed the SSL Encryption level to 128 bit or higher & Signing to SHA512

I then generated a new self signed cert with 2048 bits & bounced the DSM SA Connection Service... still no joy on the RC4 cipher... that turns out to be:

Edit "C:\Dell\ServerAdministrator\apache-tomcat\conf\server.xml" & remove "SSL_RSA_WITH_RC4_128_SHA,SSL_RSA_WITH_RC4_128_MD5" from the line:

Save & bounce the service... this all leaves me with  SSL Certificate Cannot Be Trusted and  SSL Self-Signed Certificate vulnerabilities which I will likely live with...

So what I need help with... is there a way to programatically generate & assign the self-signed certificate?

I need to do this to my entire fleet.