Had this problem several times, first time did the same thing as Kerri, piece of scrap feel to the side and when gantry moved forward it lifted the pop up pin and then crash (model 43).
head was out of tram at this point, 400$ service call was put in, tech guy used the tram bar and dial indicator technique.
Have since made my own "L" bar and do it myself.
Procedure is fairly simple, attach bar to tool holder and zero in dial indicator about 8" away from center.parallel with y axis.
Very important, at this point mark the location of your dial indicator on wasteboard (vacuum on also)
now rotate dial 180 deg, and now you need to move the y axis about 16" or so (will vary depending on where dial indicator is on bar) so that it lines up with the mark you made on wasteboard. this will give how much your off, divide that in half and that how much you need move your head by.
This is how the techs do it.
Last time this happen I was well over 0.200" off (like i sais serious crash). I actually had to remove the head completly to realigned the block behind the one that hold the head. if your only off by 0.030" , there should be enough play in the holes to fix that.
But in removing the head i created another problem and that is my head is now slightly more to the right then where i was and now my pop up are off. this affect my nested flip operation and still have to get procedure now to fix that.
hope that helps