Has any research lab done serious work to engineer new bacteria which assemble graphene wafers?
Surprisingly, the answer is yes. In 2012 Tanizawa et al published a paper titled Microorganism mediated synthesis of reduced graphene oxide films. The gist of it is that most of the steps (including the structuring of the graphene sheet) were carried out with chemical synthesis, but a final reduction step from graphene oxide to graphene was carried out using bacteria from a local river.

Probably not quite what you were thinking of, but I imagine this is the closest you'll get for right now.