I would price up your car at New Mercedes Benz E Class Cars for Sale | Cheap Mercedes Benz E Class Deals | E Class Reviews
and use it a as a guide to negotiate with the dealer.
My Dad picked up a new C class Executive SE from them a few weeks ago (new build). Got a 15% discount and the car was sourced from Mercedes Corporate. It also came with the expensive ridged car mats for free !
I don't think the discount they offer on the E class is as much but probably still competitive.
They have a stock (which may mean pre-registered) 350 CDI Avantgarde with Command Sat Nav and Airmatic suspension for £36,995
Mercedes Benz E Class E350 CDI BlueEFFICIENCY Avantgarde 4dr Tip Auto Diesel Saloon New Car - in stock
Did you look into the E350CDI they had in stock (above) - it sounds like a good deal for a car that appears to be well spec'd and a diesel engine