I don't have all of the answers to above, but this link was posted about two weeks ago, and I found it helpful...
http://tiltforums.com/t/star-trek-wiki/456/43
Pasted below:
Multiballs
The black hole shot to the right of Vengeance will add a ball once during multiball when it is lit. Light it by shooting the ‘red matter’ targets around the play field that you’ve ultimately hit plenty of times cause you’re bad and you missed the ramps and loops.
Klingon Multiball
The 3 green standups light locks at Vengeance and/or left scoop. Lock 3 balls to start Klingon multiball. All shots start out lit for jackpots. Once a shot has been hit twice, the corresponding ship on screen is destroyed and that shot unlights. The 7th jackpot is a Super Jackpot worth 6.25M. The 14th (final) jackpot is another Super Jackpot worth 10M. This is followed by one roving shot worth 4M. Finally, the warp ramp will light for a Double Super Jackpot worth 20M. Completing this shot will earn a single gold medal. Then the mode restarts.
Vengeance Multiball
The first Vengeance mode is “Vengeance Multiball.” This is activated by hitting the Vengeance shot when the target is down and the arrow is white. The ball will be caught by a magnet, and a second ball will be auto-launched. Hit the magnet-held ball under the Vengeance ship at the start to add a ball and extend ball save time. Shots to Vengeance and lit white shots do damage and award points. Defeating Vengeance by completing enough shots and then hitting the Vengeance shot awards 5M multiplied by combo and/or 2x scoring. After defeating the Vengeance, multiball will continue with victory laps in which the goal is to make all seven major shots over and over.
Kobayashi Maru – Level 1 Mini-Wizard Mode
Once all level one modes have been completed, the Vengeance shot will light white for Kobayashi Maru. Starting KM will immediately award you medal bonuses based on medals collected so far (see below). This begins as a 2-ball multiball with all shots lit except the Warp ramp. Each shot requires 2 hits to clear it out – the first shot is nominal points (250K?), the second shot is based on your performance in the corresponding level 1 mode (arrow color tells you which mode). Clearing them all out allows you to continue in single ball play even though you have more than one ball active on the playfield. Shots in this mode max at 7.5M.
The medal bonus awarded for starting the mode is as follows:
Set of 6 Bronze medals = 10M. Otherwise, each bronze is worth 1M up to a set.
Set of 6 Silver medals = 20M. Otherwise, each silver is 2M up to a set.
Set of 6 Gold medals = 35M. Otherwise, each gold is 3.5M up to a set.
Advanced Multiballs
Enterprise Amok
Once all level two modes have been completed, the Vengeance shot will light white for Enterprise Amok. Starting Enterprise Amok will immediately award you medal bonuses based on all medals collected so far. This begins as a 2-ball multiball with all shots lit and a switch hit counter on the display. Completing the number of switch hits required will add a ball into play (except for the 6th and final round) and light all shots white for a final shot. The next shot hit will then be unlit for future final shots in the mode and will start a new higher switch hit requirement. After completing the 6th and final round, the Vengeance shot will be lit for a Super Jackpot. Completing this final shot allows you to continue in single ball play even though you have more than one ball active on the playfield.
Five Year Mission
Once all level three modes have been completed, the Vengeance shot will light white for Five Year Mission. Starting Five Year Mission will immediately award you medal bonuses based on all medals collected so far. This begins as a 4-ball multiball with all shots lit and…
Vengeance Modes
Hitting the Vengeance drop down target or lane underneath the ship or firing photon torpedoes will advance toward a Vengeance mode. The three modes always occur in order and repeat after playing the third mode. If a Vengeance mode is lit when the ball drains, a new mission cannot be selected before the plunge on the next ball and will have to be started by shooting the left eject hole or the Away Team shot.
Photon torpedoes can be earned by lighting all three orange spot targets on the right side just below the upper flipper. Lighting the targets grants three torpedoes, and up to eight can be amassed at one time. Press the Fire button on the lockdown bar to use a photon torpedo against the Vengeance. If a Vengeance mode is already lit, no more torpedoes can be used until the mode starts.
Vengeance Multiball
The first Vengeance mode is Vengeance Multiball. This is lit by hitting the Vengeance shot 5 times (the first time); credit toward these hits will also be given for each photon torpedo fired (see Vengeance Modes below). To start the multiball, shoot the Vengeance when the target is down and the arrow is white. The ball will be caught by a magnet, and a second ball will be auto-launched. Hit the magnet-held ball under the Vengeance ship within 15 seconds to add a ball and extend ball save time. Shots to the Vengeance and lit white shots do damage and award points. Defeating the Vengeance by completing 10 white shots and then hitting the Vengeance shot awards 5M multiplied by combo and/or 2x scoring. Photon torpedoes can be used toward destroying the Vengeance but will not count as the final shot. After defeating the Vengeance, multiball will continue with victory laps in which the goal is to complete all seven major shots over and over.
Vengeance Scoring
This second Vengeance mode lights after any combination of 6 hits (the first time) to the Vengeance and photon torpedoes fired. To start the mode, shoot under the Vengeance when lit white. The mode consists of 5 hurry-up shots, all at the Vengeance. Each shot will be quickly thrust back toward the flippers. Completing all 5 hurry-ups grants an extra ball.
Vengeance Battle
This third Vengeance mode lights after any combination of 7 hits to the Vengeance and torpedoes fired. To start the mode, shoot under the Vengeance when lit white. Then five more shots under the Vengeance are required before entering into Sudden Death. In Sudden Death, the drop target will be raised. Shoot the target and then under the Vengeance within 6 seconds to finish the mode; otherwise the target will reset. The reward is the greater of 10M or 10% of your total score, times any combo or 2x scoring multiplier. This mode will only end if completed or if the ball drains after starting Sudden Death.