Maxim has been building his own traps and has written a more complete alignment guide. I'll try and post more information here as updates come up.
Another useful file from Maxim and Steven Wasserman to aid in OT assembly, the following is a PDF of the optical trap footprint with a dot grid representing the tapped holes in the breadboard.
File:Optical Trap Footprint.pdf
--dapple 17:16, 23 August 2007 (EDT)