Dealers don't make much on the recall from central Toyota, so this seems like the perfect opportunity to make the job worthwhile for them. The baffle plate in particular seems steep, even if it were two hours work, that still works out at over a hundred quid an hour labour, with VAT knocked off. Unless you're desperate to only have dealers hands on the car (which would be daft if you're doing mods) personally I'd make them do the bare minimum required to get the recall done, at no expense to you and then get your aftermarket bits done by a good indie. It's not like manifold, overripe or baffle require specialist knowledge of the model.