This is definitely a challenging stage, perhaps too much so for where it is in the adventure, and likely seems a bit too reliant on luck for most players, but there are definitely some strategies that are very helpful.
The stage imposes a 2 minute limit on you, which means you need to act fast, but try not to feel too rushed; the best way to succeed here is to take your time to set up large color-reactions. By right clicking on blocks to dim other colors, it is a lot easier to see what blocks are on the playing field. You usually want to be working with whatever color is the most plentiful, so that can be a helpful trick to quickly scan the different colors. Once you've selected a color, you want as many blocks of that color to be touching as you can, so it can be very helpful to clear out a few blocks of other colors, dropping blocks down to join together clumps of your color. When doing this, you want to remove as few blocks as is reasonable; the more you clear, the harder it is to manage the aftermath. If you only clear 3 or 4, it's significantly easier to keep things from getting out of control. Also think about which blocks you want to pick for clearing the color-reactive block; by picking a good starting point and clearing a couple more blocks without color-reaction, you may include another clump that more than makes up the for blocks that you used for the chain.
When you clear one of the color-reactive blocks, you'll have a lot of mayhem on your hands and need to do some damage-control. Try to keep the blocks near the special blocks pointing away from the special blocks in order to protect them. If you lose one, it's not that big a deal, but losing a second one will leave you unlikely to be able to hit the 55-block target. Don't expect to be able to plan everything that's going on when all of the blocks are falling; instead, just focus on keeping the special blocks safe, which means focusing primarily on their immediate vicinity.
This stage is much more of a thinking-man's stage than most of the rest of the game. It benefits from a lot of planning and deep thought, and in that way is a lot like one of the brainteasers. However, the time limit and randomization ensure that you can't plan out every aspect of it, so reflexes are very helpful. Approach it with a good general plan and I suspect you'll be able to conquer it. :) With some practice, you'll hopefully be able to finish it every time you try.