New Bike + Disc Brake Shuddering: Cause and Fix? I recently bought a new bike (cx steel frame, carbon fork, disc brakes) that I am using as a commuter/all-rounder bike. 

My question is similar to questions that have already been asked concerning disc brake shuddering/pulsing (here and here), but subtly different: Will skipping the bedding in process lead to shuddering when braking? If so, will attempting the bedding in process now fix the issue?

I am new to the world of disc brakes and foolishly didn't learn about bedding the pads until searching for resolutions to my issue. I have ridden my bike for ~200 miles so far, and the past 50 miles is when the shuddering in the front brake became noticeable.

Brake Details: I have Hayes CX Expert mechanical disc brakes and a carbon fork.
Skipping the "proper" bedding in process can do this yes. Bedding in brake pads impregnates the rotor surface with material. There is a particular process to do it because you want a good even layer. If skipped, the will still get "bedded in" but possibly unevenly, causing vibrations and ultimately a shudder like you have described as the pads skip over these slightly thicker portions of the rotor. The proper method has guidelines of how fast and how hard to brake which has been proven to help keep the bedded layer smooth. Also if not bedded in and then ridden EXTREMELY hard brand new, meaning some downhill action,it is possible (but unlikely) to get hot spots much like car brake rotors can get when super heated beyond their intended use. 

Their are several ways to handle this situation, there is a resurfacing paste product called Squeeel Out that works decent, or you can resurface them yourself which generally works pretty well. To do so you will sand both the pads and the rotor surface, and then follow the initial bed in procedure. 

When sanding the pads, it is easiest to lay a piece of sandpaper on a hard flat surface and drag the pad around in circular motions. Sand the pad directly doesn't work as well because you don't get an even sanding. The rotor can be done a similar way, or by laying the rotor on a flat surface and hand sanding with a sanding block. You don't have to take a ton of material off, just remove the surface contaminants. After sanding the rotor clean with alcohol and allow to dry. 

Some people would recommend buy a new rotor and/or set of pads but i have had good luck with saving them the ways mentioned above. While you have the rotor off you can also check that it is true, but that shouldn't be an issue with it being new, but then again i have seen them come out of the package slightly bent.