Here are the tweaks I did on my very early production Alien: (re-posting from official thread)
1) Playfield LCD - You MUST make sure the LCD is level in the playfield, as you risk playfield chipping on that edge if it is not. The issue I had was despite making the adjustment (just four screws holding the LCD), it would not hold it's position. After 20 or so plays, I'd lift the playfield, and one of the LCD mounting screws would have fallen out into the bottom of the cabinet. The easy fix was to use small lock-washers between the playfield and the LCD mounting bracket. My LCD has been level and stable since.
2) Pops and slings - As with any new machine, you will want to gap the leaf switches for the pops and slings.
3) Airlock scoop - This is a very important shot in the game, as it starts all of the modes. Mine was firing SDTM more than 50% of the time - not fun. There are several ways to adjust a scoop. I loosened the mounting screws and tried to 'twist' slightly - but there really wasn't much room to adjust, so I went overkill - removed the mech and used a drill to slightly enlarge the mounting holes. That gave it enough play to adjust the trajectory of the ball.
4) Shooter lane ball kickout - About 10% of the time, my game had some trouble getting the ball into the shooter lane. I found that the lane protector (mounted on the shooter lane with two screws) was slightly overhanging the ball trough launch. I didn't want to try re-mounting it farther back fearing I could mess up the shooter lane. Instead, I removed the protector and tested that indeed it was the issue. I then took a dremel and ground it down just a bit to remove the little bit that was overhanging. Re-mounted it, and haven't had an issue since.
5) Upper rt flipper - was not returning to rest position 100%. I installed a slightly stronger spring - fixed.
6) Playfield switches - My top rollover lanes were not registering. This was because one of the PCP's was not mounted completely flush to the playfield. The proximity switches that are under the playfield need to be completely inside their mounting holes. Tightened everything up - easy fix.
7) Ramp feeds to inlanes - I made a tweak to almost completely eliminate the frustrating 'ball hopping out' when it should feed cleanly from the ramp to the in-lane. The ramp exit hole is a teardrop shape. It is so big, the ball comes out at and angle rather than a drop and rattles out sometimes. My fix is gonna sound cheap and stupid, but it has worked 100%. I cut some thick black cardboard from my gopro box and used black electrical tape to tape it to the underside of the ramp. It is just enough to cover the 'tear' part of The hole, making it smaller.
8 ) Leveled the machine. Yep - that helps.
9) Mylar around the airlock scoop
10) Xeno mech - currently disabled...waiting on new Xeno mech/board.