I used to be one of those people that timed the modes out on level 1 (yeah I know I know!

) but the new code prevents that. You are rewarded for playing the modes and the more shots you hit the better a medal you get. Generally it works as:
Level 1 > Play modes. If you're going for the long game attempt to do 2, 2 then 1 to get 2 bonuses instead of 1. What I mean by that is in the honeycomb style mode layout play Space Jump, Prime Directive, Nero and Destroy the Drill and then link those up with Save the Enterprise. This will give you for example both Super Spinner and Super Ramps (I forget which one the 3 in a row completion awards for a particular row) rather than just 1 of them. Then finish off with Klingon Battle and then go for Kobiyashi Maru Multiball. A good idea like most people say is to play a multiball to help you finish a mode but I think some people try to save these for other things. You can do this in 3 combinations for the modes depending which 2 bonuses you want to pick up.
Level 2 > This was generally where I would crap out, I never made it to Enterprise Amok but I would have though try to employ the same strategy to get there. It's just much harder as you HAVE to finish these modes for them to count or they time out and you have to carry on via a restart by shooting the mode start hole or under the left flipper into the shooter lane. I think I finished 5 modes at level 2 once and that was the best I managed.
Don't forget to hit warp ramps, I think depending on the settings warp 9 is 2x scoring for 20 seconds and 9.9 is a special multiball.
I always found that the Vengeance Hurry-Up was death because it is a single ball mode where you have to shoot the ship and it just fires it straight back at the flippers and often sends the ball screaming out of control.
Good luck Sarge
Edit: Also best quite "Dammit Jim I'm a Doctor not a Pinball Wizard!" from Karl Urban always put a smile on my face. What is everyones faves?