Hi @latintrpt
I'll gloss over the part about self-signed certs because that is usually not a good way to do anything, other than for quick and dirty lab testing.
You can convert a cert in PEM format into DER format (aka PKCS1) using openssl - (the syntax varies by which version of OS you have it installed). Using Ubuntu it would go like this (where the input file is Defaultselfsignedservercerti.pem, and the output file is cert.cer)
openssl x509 -in Defaultselfsignedservercerti.pem -outform DER -out cert.cer
Every version of iOS may be different but the last time I had a look, you could email yourself a cert, and install that cert into the trust store. Then you select that cert and tell it that you want to trust it. It's a two step process.
Probably better done with an MDM if done at scale. Apple Configurator is great but not quite designed for mass deployment purposes.