Both my diesels smoke upon start-up, especially in winter. It's slight over fueling to compensate for the low ambient temps. Nothing you can do about it.
My R5 had an elusive misfire on one cylinder for about a month which totally baffled two dealers. I eventually traced the fault to bad quality fuel. The filling station regularly used, had water in the underground diesel tanks. I changed to SASOL 50ppm from a reputable filling station and the problem went away.
BTW, I only put 2 and 2 together when my TDI Jetta also started misfiring.