Upper pulley on rear derailleur (jockey?) very close to cassette?
Several things coming to mind when I read this. 

a) If the wheel is not centred, its not sitting in the drops correctly. If its not sitting in the drop-outs correctly, the axle to derailleur mount distance and the angles of the derailleur to cassette are off.  There is little point looking at derailleur adjustments unless the wheel is centred.  

b) Smallest smallest is cross chained. Performance of derailleur in this state is relatively unimportant 

c) The derailleur was properly adjusted before the wheel was removed.... The thing that affects the clearance of the jockey wheel is the B screw - was this changed? 

The first thing to do is put the wheel on straight, remove the cross loading by putting the dérailleur onto the largest rear cog, and if needed, adjust the B Screw.