Can you take this as a learning experience?
1. Tools to encrypt messages using Github SSH keys are probably not a good idea. They're no more usable than real message encryption solutions, but have far more constraints.
2. You cannot safely use RSA like a normal cipher. RSA is a tool for building crypto protocols. The way you've deployed it here has a serious vulnerability.
If you want to build things that use cryptography, I think you really need to work with a high-level library. Nacl (or libsodium) is a great example of a package that goes out of its way to bulletproof itself.