I'm no employment lawyer, but your language is all over the place here, and before you make enquiries you have to get your story straight.
If you're 'self employed' the person paying you isn't your employer, they're your primary contractor, and what they pay you isn't 'wages' it's your fee.
But from the sounds of this, you're not actually self employed at all, if everything to do with this 'job' is in the control of your 'employer' then you're employed, but they're trying to avoid being an employer for their own convenience. There's better guidance on HMRC's website, but basically if they're responsible for giving you work, training, they control your holidays, you don't have autonomy to hire staff to do the work for you or negotiate when and how it's done, then you're probably an employee.
Back to your question, as above, if you don't know what they should be paying you, how would you get to find out? All of that should have been stipulated in the contract. In fact, there should be a fresh contract for each 'job' they give you. It's time to sit down with them and ask how this is supposed to work.