Thanks very much for all your responses - it's very helpful!
Just to let you know that this plumber was recommended to us and that they have invoiced us almost £950 for this - it's not cash in hand and we didn't intend to have employed a cowboy
We've learnt a lot from this and will look out for professional membership next time...
We are currently writing a letter stating why we're not happy. We haven't paid them yet and are considering offering half the amount and calling it a day... I'd rather pay and have a professional come and fix it instead of them back again.
Regards the wonky toilet, I mean wonky in that it is not at a right angle with the back wall. It's also 6 inches plus from the back wall... is that normal? It doesn't have any holes in the cistern to attach it - you're right. So the plumber has attached two pieces of wood as a bumper on the wall which don't make contact with the cistern, to prevent the cistern from cracking.
Re siting the toilet, perhaps we didn't specify it enough at the beginning, I just assumed that they would replace each piece like for like, so put the new toilet where the old one was.
Re the basin pop up, I suggested that perhaps the supplier had sent us the wrong part and could they check that rather than waste 1/2 hour trying to figure it out but they didn't seem to want to contact them... I guess, with hindsight, in case their incompetence was highlighted!
Oh well, a lesson learnt I guess. Thanks again for your advice.