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Fuel consumption is not an issue which has concerned me in the past. I know the reserve light comes on about 130 miles after the last fill up. I did once measure it and it was about 45 mpg when commuting and approaching 50 mpg on long runs. However the right cylinder head recently failed after 100k miles and thus in view of the mileage I obtained an engine with 27k miles on and had someone fit it. The bike runs very well with no severe vibration, it ticks over, it starts easily and there are fluid no leaks. However it seemed to need refuelling more often so I measured consumption over the last 3 refuels. It is returning less that 35mpg for use which is currently a commuting run of 15 miles, 9 of which is on a dual carriageway, which is sometimes busy.

I could, and will if necessary, dig deep and have the timing and injectors setup checked by a BMW dealer, but does anyone have an ideas?

I get closer to 40 mpg, so 35 isn't that far out. May just need a tune up as you say, in order to get close to your old engine.
Maybe take out the plugs to check the colour?
Any build up yet on the exhaust? The lambda sensor connected okay?
Maybe just an Italian tune up needed?

Should be about 10mpl; better on a long, steady, run. On a properly serviced bike.

Did you get a complete engine fitted with throttle bodies injectors etc or did you transfer all the ancilliaries. All you can really do or get done is check the air filter , valve clearances , plugs , balance the throttle bodies and check the TPS voltage.