The recent change for babies due from October 2008 was to ensure that mothers are now entitled to benefits throughout their maternity leave, rather than just in Ordinary Maternity Leave.
However you are not entitled to remuneration during maternity leave, and it's not clear at the moment as a matter of law whether cash benefits like car allowances are remuneration. I think at the moment the most recent case indicates that car allowances are considered remuneration and therefore not payable during maternity leave, but it's still up for debate AFAIK.
However, you have an excellent argument for three reasons.
Firstly, (assuming this car allowance is given as an alternative to a company car) you would be entitled to a company car throughout maternity leave, therefore you'd argue that you should similarly be entitled to the car allowance throughout maternity leave.
Secondly you have the moral argument that the car allowance is (presumably) funding some sort of car loan or lease, an obligation which you cannot get out of just because you are on maternity leave.
Thirdly you also have the excellent argument that your employer has clearly indicated that it views your car allowance as a benefit, not as remuneration, as evidenced by the fact that they have continued to pay it during Ordinary Maternity Leave, which they would not have done had they considered it to be salary.
Those arguments are dependent on the fact that your baby was due after 5th October this year, although you could still argue the second point regardless.
In terms of KIT days, these are not a legal entitlement, they are a tool to be used with the agreement of employer and employee. If you wish to use them and your employer agrees, then fine. Payment for them isn't automatically your normal salary payment, it would often involve a top up of SMP.
But if your employer doesn't find it convenient to have you back, they don't have to allow them. I'm not sure what this time in lieu is, that seems bizarre. Either you are using the KIT days for the purposes they were intended or you are not, time in lieu is not either a requirement or sensible. You will have accrued bags of holiday during maternity leave anyway so I'm not sure how giving you extra paid days off is a good idea.