Funny I am trying to solve all of these exact problems for my Surly disc trucker..

For the rear rack I purchased the Jaand rack but may swap it out for the surly racks.
I have purchased the Ortlieb rollup waterproof bags and so far they are fantastic! You can find deals on them at REI
I did not want clip-less pedals so I purchased sabot pedals from velo-orange (I have wide feet)
Getting ready to purchase fenders and from my research I plan on purchasing the SKS P50 fenders as I believe they support tires up to 45mm but they may need added mudflaps

Hope it helps...