To whomever it may concern I resolved this issue by using the PublicKeyFactory and SubjectPublicKeyInfoFactory to encode and decode the key.
Using:
byte[] key = SubjectPublicKeyInfoFactory.createSubjectPublicKeyInfo(pubKey).getEncoded();
I was able to get the raw bytes of the key.
and using:
ECPublicKeyParameters bpubKey = (ECPublicKeyParameters)PublicKeyFactory.createKey(key);
I was able to recreate the public key.