A bit late with my answer but here goes anyway:
You already used two files on the screwdriver to make it work? Have you opened the top of the bomb already?
The cover:
Spoiler:Use the flat file and the round file to make the screw driver suitable for the screws. Use the fire extinguisher on the motion detector to freeze it and quickly unscrew the screws. You may need to use the extinguisher several times if you are not fast. After all the screws are loose you used the screwdriver again (I think) on the side to lift the cover.
If you already opened the cover and are stuck with the plastic cover inside:
Spoiler:First thing you need to cut the right wire to disable the bomb. There is a hole in the plastic in the middle of the bomb. I think it was the lowest wire but you can just follow the wires to see the correct one. The paper which had the laser guide also had a guide for the bomb. After disabling the explosive you need to unscrew the hex bolts with the key you found from level 0. When you lift the plastic cover away you need to stuck the last file on the clock mechanism to stop it.
You can also ask me about the AoM2, I just recently played the trilogy.
