However, the written offer has now arrived and I am not at all happy to accept many of the T&C's within the contract. I won't go into detail, but suffice to say these are not financial and directly contradict some of the answers I was given during the interview and relate to areas that are important to me. Furthermore this is not something I'd feel comfortable negotiating as there are numerous points of contention, and to be honest I am not sure I'd be happy to work for a company that have not been honest about many aspects of the position.
I'd outline the bits you're not comfortable with... you'll very likely find if you've got an issue with a significant amount that they can't budge either... you then decline on that basis. Tis then more on them, you were happy to work for them but then they've thrown in a bunch of extra conditions and mislead you... well they're the ones changing the situation.
It might also be the case that the standard company contract states one thing but the team works in a different manner - ergo the hiring manager might not have lied to you. Then again if that is the case it isn't necessarily ideal as you may be there for some time and change teams etc.. and the new manager of the new thing might run things differently, you contract which didn't matter before (don't worry about it says your first manager, we run things differently in this team) now does matter.
Working time directive opt out ought to be a separate form and not included in your contract IMO... it is voluntary - but I guess they might encourage it with shift payments/bonuses