hmm...I personally find it hard to believe that you scored 999,999, but I'm not saying it's impossible. This weekend I'll do some "research" by riding the ride a lot to see if I could figure out what gets you all of those points.
Some hints for the ride (not really secrets) are to, of course, press the red button right before you get swallowed. Also After you get scanned and they tell you to shoot the other car, look up. There are small aliens holding guns. You must shoot both of these before they shoot you, or you will spin and your guns will be disabled momentarily. (they also get you alot of points).
Some little know facts about the ride are that after you travel out of the training room, and you are in the city room, on the right side, there is an alien holding a newspaper that's headline has to do with jurassic park. The Head that the aliens are holding is of speilburg (kind of like George Lucas in star tours). I've attached a picture of it. When the ride first opened, this wasn't there, but it was his request to put it in.
Also, there are many endings to the ride. First, there are different videos of will smith saying who won. Then, most of the time you will turn to the center when you get talked to by the animatronic "boss" alien telling you what you did wrong. If everyone in your car scores over 150,000 pts. (on average), you will turn to the outside and see an alien trimming you "MIB SUIT." This alien says two things, different each time. With either ending, your memory always gets erased.
below, you'll see a picture of the speilburg alien. Sorry it's bad quality.