First thing you'll notice, my locomotive is red not green- I do 
not have a stock Emerald Night handy, but this is just a 
repaint. I am also starting with gray rods on my repaint, they 
should be black on a stock Emerald Night. The final rods should 
be gray, using the colors shown in image 07. The custom rods 
used in this mod are available at: 
http://www.bricklink.com/store.asp?p=zephyr

Walking through the photos of changing the rods on one side (x2 
for the other side):

01) start with the patient (do not spread your bricks in the 
lawn, mix your bags, etc.)

02) pull off and disassemble the existing rods (on my repaint 
they are gray, but they should be black on a stock Emerald 
Night)

03) pull off the bind driver and front driver, remove the red 
rubber band from the front driver (it might have turned black if 
you've run your engine a lot)

04) set these parts aside, you will not need them

05) keep one full technic pin and both technic 3/4 pins

06) insert these pins in the wheels as shown

07) here are the new parts you will need. Note that the technic 
axle is 7 long. All of the new parts should be light gray.

08) attach the side rod

09) prepare the connecting rod- note that you should insert the 
half pin through the front of the rod

10) attach the connecting rod as shown

11) Voila


There are many possible combinations that would work. I chose to 
use the 7 long technic axle in this example because it is a 
fairly common part. The gray 6 long axles seen in photos 01-04 
were discontinued several years ago and are harder to find. If 
you prefer a 6 long axle, you could use an 8 long connecting rod 
instead of the 7 long used in this example. You might even be 
able to use a 5 long axle with an 8 long connecting rod but 
there is a greater chance the technic axle pistons will jam. I 
highly recommend the cylinder modification from RailBricks #7. 
As an addendum to that article, you can also eliminate the wheel 
clutch issue using bushings inside the frame.