MAW,
I have a 40 550, but have never removed the shock spring. But its Sunday, and you want to do this today, right!
From looking at the parts manual, I would do the following:
1. Remove the shock from the bike.
2. Loosen the clamp screw in the top spring retainer.
3. Back the top spring retainer up to the top of the shock. Your 04 tool kit had a flat wrench for doing this.
4. Turn the shock upside down, and separate the 4 items on that end of the shock. If you look at page 25 of your 04 parts Manual you will see them. Once they are separated, the item 43 spring retainer should slip off from the shaft, allowing you to remove the other 3 parts and the spring.
5. After reassembling the shock assembly with the new spring, set your sag per page 32-34 of your owners Manual. Remember to torque the clamp screw in the top ring per page 34. Eight Nm is 70 inch pounds.
Let me know if this helps!
Joe