After a little help from a VAG expert!

Got this A4 TDI in, complaints are a REALLY rough idle (shakes the whole car) and really bad smoking (black). Report was car running fine, then a sudden power drop accompanied by lots of black smke from the exhaust. Did a fault code scan and came up with 3 codes:

16485 Mass Air flow sensor, implausible signal
16683 boost pressure regulation: control range not reached
16686 cylinder 2 misfire detected

I traced 2 out of three codes to a broken EGR flap which has now been renewed. A smoke test of the turbo/intake system shows no leaks.I still have the rough idle and the cylinder two misfire problem. Looking at the fuelling values for the 4 injectors shows:

Cyl 1 -1.29mg/st
Cyl 2, 2.99mg/st
Cyl 3, 0.24mg/st
Cyl 4, -2.31mg/st

Number 2 and 4 seem out to me - any ideas?
I've checked the injector current on the multiplug at the rear of the head and all 4 signals look like they are present. My next step is to check the in-head injector loom.

Any advice on from the VAG collective greatly appreciated.