I seriously doubt that you're screwed. I've disassembled and re-assembled my Sebenza more times than I can remember. I've only taken two Emersons apart, but they were even easier to re-assemble than my Sebenza. All three knives went back together in EXACTLY the reverse order of how they came apart. Here are some tips. Read ALL parts before you start!
1. RELAX.
2. Wash and dry EVERYTHING.
3. Apply a small amount of lube to both sides of the bushings and the areas of the blade they'll contact.
4. Apply a small amount of lube to the primary and secondary detents.
5. Apply a small amount of lube to the blade pivot.
6. Lay everything out so you can easily see it.
7. RELAX.
8. Start with the lock side. Push the pivot through the scale, then into the lock side scale. Place the pre-lubed bushing on the pivot. Place the pre-lubed blade on the pivot. Place the other pre-lubed bushing on the pivot.
9. Place the stop pin in its hole.
10. RELAX.
11. Put the non-lock slab and liner together. You now have two halves of a Commander, some screws, and a backspacer.
12. RELAX.
13. Lining up the stop pin and the pivot, assemble the two 'halves'.
14. Put in the pivot screw first. Screw it in a little, but do NOT tighten it.
15. Place the backspacer between the two halves. Carefully start the screws that go through it. Screw them in a little, but do NOT tighten them.
16. Look at what you've assembled. Make sure the stop pin is not crooked. Make sure everything looks and feels right.
17. Tighten the pivot screw until you feel a little resistance. Tighten the other screws until you feel a little resistance.
18. Repeat step 16.
19. Tighten the pivot screw until your blade moves EASILY. Tighten the other screws. Flick the blade open a few times. Tighten the pivot screw until your blade moves like you want it to move.
20. Install the clip.
21. RELAX.
Let me know how it goes.