I have found that it is easiest to re-align the drive in the unloaded position.The "arms" (on which the rubber wheels are mounted) need to complement the position of the lens.
Unscrew the plastic piece on which the arms are mounted, and you can move the gears manually. You will notice that there are two pins that raise up when the lens is in the reading position. You should align the mechanism so that these pins are laying flat. You can then re-attach the arm board without having to move the arms into any special position.
Plug the console in, and turn it on. The gears should start spinning. If they do not, press the eject button. If that checks out, place the top half of the blu-ray drive back on the drive, and try inserting a disk. If it goes in, your good to go. If it makes a horrible crunching sound, you will have to go and try again.
I have re-aligned several Blu-Ray drives, and each one has been a little different. Try a couple combinations of ejecting, powering on and off, and tripping the sensor, both with and without the arms attached.
Best of luck, let us know how it works out.