Ah very good.Illusionary pain only occurs within the mind whilst physical pain has effects which manifest themselves in reality. The former just makes you experience the sensation of pain without producing injuries/wounds on your body.
I think a genjutsu can produce physical pain in two ways which are:
-Placing an intense amount of stress on the mind (Often known as Demonic Illusions)
-Producing bodily reactions which prove to be harmful e.g. coughing, wheezing, vomiting and etc.
Okay, the main attribute that differentiates Physical Pain from Illusionary pain is that Physical Pain will always have a reality pull, if you're unsure of what's real and what's not, Physical Pain can and will always be able to act as your anchor. Like I said before, Genjutsu tries to mimic reality, but it cannot create reality, so it can mimic pain, but it will never create pain. With that being said, the number one thing you need to have in mind is that Physical Pain will break you from a genjutsu and creating a "chakra spike" while Illusionary Pain will not. It can battle a Genjutsu due to how Genjutsu reacts to other Genjutsu, but it can not create a spike.
But Genjutsu can create physical pain. Given that you're forcing the brain into seeing things that do not exist, the higher the dose of chakra, higher the rank, or higher the time your opponent is under the effects of a Genjutsu, then higher the strain on the brain. And that strain can be translated into headaches, Physical Pain. Any genjutsu can do that, as long as it is high enough or lengthy enough (Which is why I believe S rank-level genjutsu acts against itself), or by genjutsu that specifically state a certain damage or a certain side effect in their description.
Secondly, like you said, while Genjutsu can't produce Physical Pain unless through brain stress, you can make your opponent hurt himself. Just as you have the power to break someone's elses bones, you can do the same with your own. So, if a genjutsu disorients in the right way, you can end up dislodging some limbs or breaking some bones. For example, you wouldn't normally twist your arm behind your back with such strength that it would break, but if there was a Tactile Genjutsu that makes you think there's someone bending your arm in such way, you'd force it to break. See it as a "Conceal" type of deal, where your sense of self-preservation is being distorted by a clone pulling your arm. Likewise, if there is a rock or root on the ground, you can have an illusion where they don't see them, or where they're led to them, trip on them and break a leg. Etc etc.
Questions?