Hi Ben,
I have repaired an X-files with a similar problem. The surrounding posts can pull out of the playfield and if crooked can blocked the opto path. The posts can also break free and hit the opto board and cause damage. You can check if the optos are aligned by looking at the red LED located on the lower part of the opto board underneath the playfield. When the boards are correctly aligned the red LED under the playfield should go out and when the beam if blocked it will turn back on. You can loosen the screws on both the transmitter and receiver boards and move them around until you find the position where the red LED goes out. You will need to check this on both sets of boards. The posts can break aways from the edges of the playfield and can sometimes be fixed by placing a washer underneath them to spread the load. The posts are needed to protect the optos from damage. The opto LEDs are a special type which glow red on Stern and Sega pinballs. If you cannot get the boards to align successfully you might need to replace both sets of optos.

regards Derek