The drop target boards are not wired right or could be changed to be better. There are two circuits on those boards. One is off-on-off and the other is off-on. Most Williams of that era had the off-on-off circuit wired in series with the other boards so it knew when all the drops we're down to reset.

Alien poker only needs one of the circuits and off-on circuit is best. If it is making a bad connection, a little vibration is all that is needed to get it to go. If the circuit is missed on the way down with off-on-off, your sol.

To me it looks like it should wired like the diagram. I have a PBL replacement board and mine are wired in the center holes. The siegecraft diagram shows center holes. Yours are on outer holes.

IMG_20170716_104703 (resized).jpg

For the flipper, check your EOS switch. Sounds like hold winding is what is bringing it up slowly. They should be touching when not powered up.

This is what's in my AP:
http://www.pinballlife.com/index.php?p=product&id=3877

Assuming all the soldered connections are good on the bulb sockets, I would think it is the connector at the board. Look for corrosion or maybe the connector is worn. Seems like it heated up and got angry at game 8.