To be honest, it helps if you add additional points to the existing question you have already raised rather than raise a new question.
This one.
http://www.theanswerbank.co.uk/Jobs-and-Educat ion/Jobs/Question760247.html
I note that you haven't answered the questions that I put to you - which would help me understand what you are up against.
However regarding your first point on this question, your employer does have a point because custom and practice does have some strength. Whether three months is long enough for you to flag this up is a moot point - there is nothing in law that says 3 months - it would have to be tested at Employment Tribunal.
Unfortunately there is nothing discriminatory about paying one job at rate X and another at rate Y - perhaps there is a global shortage of labourers? (I jest).
However this doesn't sound like a good organisation to be working for, so perhaps it is time to get another job. If you could do that, you could 'afford' to resign and claim constructive dismissal, perhaps.