Thanks to CAL 50 for this outstanding post I was able to fix my trunk too. Was very loose and not aligned properly anymore. Found the issue was due to one of the set screws inside the gearbox was not tight. Thought I'd share a few more pics for those folks that maybe did not take enough during the dis-assembly process.
Also, note the pic of the 3/4" wrench removing the top 2 trunk frame nuts. It was easy when I used a box end/open end wrench, then added some torque to remove by inserting a screwdriver shaft and twisting. You'll need to hold the trunk frame at the same time or it will simply spin the gears on the motor (probably not good for it).
Wrote an "F" (see pic) with a sharpie on the "Face" or "Home" part of the the trunk frame that faces the player to make certain I re-installed it that way - it helped (my memory is short)
I added my aluminum opto interrupter (bought it ages ago) and alignment was fairly straightforward and for me was driven entirely by getting the 2 nuts on top on with the trunk facing the way I had it when I removed it (home position). Then turning the opto interrupter either left or right, temporarily tightening the set screw, then running the trunk test to let it "settle". The slot in the opto interrupter will tell the motor to stop turning when it lines up with a set of optos. In my case, the opto board needed the interrupter slot to be positioned at the top (top opto, facing the flippers) in order to have the trunk in the "home" position.
Don't forget that there are 3 large washers in total at the top of the shaft (2 underneath the "top of the playfield trunk bracket" and one underneath the 2 large 3/4" trunk bracket nuts to go between the nuts and the bracket itself)
Wish I could remember which way turning the interrupter impacted which direction the trunk then "moved" but you'll see it as soon as you try it and I did not have to move it much (3/8" maybe). What you're doing is moving the "slot" on the interrupter that then allows the shaft to rotate to a new position. In other words, you're not "moving" anything when you adjust the orientation of the trunk, your just setting the opto slot to a spot that delivers an optimum trunk alignment (hope that made sense)