Having looked at both the images you've posted it seems like you are getting to grips with the set up! Have fun... only too happy to be of some help :-)

I would suggest setting the camera to manual, ensuring that the shutter is set to a speed equal to or less than that recommended for flash synch in your Nikon manual (my Olympus manual suggests 1/180th of a second or less, I usually set it to around 1/100th depending on the ambient light). Set your aperture according to whichever one of the auto settings you have selected on the Metz (having set the ISO to match the camera setting). Then just let the sensor on the Metz do the work. If using bounce flash I often use the second fill in flash on the CT45 too. You may need to experiment a little with the setup at first, but it should give consistent results in the end!

http://www.amazon.com/SP-57DUZ-SP-560EZ-SP-550EZ-SP-510EZ-Compatible/dp/B004G47I88/ref=sr_1_1?s=electronics&ie=UTF8&qid=1357297268&sr=1-1&keywords=Hot+Shoe+Safe+Sync+Adapter

I use one of these with my Metz 45CL4 and Olympus E600. Works just fine and cheaper than the Wein!

The shadow control in Snapseed is one of the best and least destructive filters I have seen. A little Topaz DeNoise also helped. I could have pushed it more than this but the noise in the really dark areas would become too obtrusive and I feel this looks more natural.

All three frames overlap perfectly. This is just a quick attempt using three layers in Photoshop CS5. Bottom layer is left picture, second layer is middle pic, top layer is right pic. Make top layer semi transparent and carefully cut away excess areas using the lasso tool with a fairly soft edge (around 3 or 4 pixels). Then the same process with the middle layer. Return both layers to nil transparency and adjust levels/curves of each layer to match brightness/contrast in all three layers. Then just flatten the image.

Are you using PC or Mac? Have you tried opening one of the files in a simpler piece of software? Can you email one of the files to me and I'll check it out?

malco555@hotmail.com

Using faster and faster shutter speeds will only result in killing any suggestion of movement in the picture. Panning with the subject is far more important. This image of a race car (not one of mine) shows what I mean. The background and wheels have some motion blur, but the car itself is sharp. This could be achieved even with 1/250th of a second!

This may be a dumb question, but when shooting the action are you aiming at a fixed point and just pressing the shutter when the subject enters the frame or are you panning with the subject? This would make all the difference. Always pan with the subject and follow through even after you press the shutter.

It seems to me as though you maybe don't have enough enough ambient light around when shooting to constrict the subject's pupils. Are you shooting in a darkened room? If you are using flash it's important to have some light available to prevent the pupils dilating and thereby reducing the area of the iris (the colored part) that can be seen.

I usually use Photoshop CS5 but often use XnView, which is a great little free application that can do quite a few image adjustments and also has batch processing that will convert between file formats.

http://www.xnview.com/

His name is Erik Johansson. Some quite complex Photoshop work going on there!

http://erikjohanssonphoto.com/

The Portraiture plug in by Imagenomic can be very useful for smoothing out skin tones and removing blemishes.

Either add a developer restrainer during processing or if already processed try using Farmers Reducer to bleach out the fog, but be very careful or you will bleach out the shadow detail along with the fog! Both these chemical should be available from a good photo store.

For future reference try to use a softer light source, a brolly or a softbox will help greatly. Also consider using some form of foundation powder makeup (even on a man), particularly on the forehead, nose, cheeks and chin.