Does your id_rsa.pub look like this?:
-----BEGIN PUBLIC KEY----- MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCqGKukO1De7zhZj6+H0qtjTkVxwTCpvKe4eCZ0 FPqri0cb2JZfXJ/DgYSF6vUpwmJG8wVQZKjeGcjDOL5UlsuusFncCzWBQ7RKNUSesmQRMSGkVb1/ 3j+skZ6UtW+5u09lHNsj6tQ51s1SPrCBkedbNf0Tp0GbMJDyR4e9T04ZZwIDAQAB -----END PUBLIC KEY-----
If so then you're authorized_keys thing needs to look more like this:
ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAAAgQCqGKukO1De7zhZj6+H0qtjTkVxwTCpvKe4eCZ0FPqri0cb2JZfXJ/DgYSF6vUpwmJG8wVQZKjeGcjDOL5UlsuusFncCzWBQ7RKNUSesmQRMSGkVb1/3j+skZ6UtW+5u09lHNsj6tQ51s1SPrCBkedbNf0Tp0GbMJDyR4e9T04ZZw== phpseclib-generated-key
Also, fyi, the SFTP vs. SSH version really doesn't matter that much. SFTP has versions 0 - 6. SSH has 1-2. SFTP (any version) only works on SSHv2.