I must be a real sucker for punishment. :) A couple of years back, I got terribly obsessed with beating this nasty game. Most of it isn't really that complicated, but Waves 9 and 10 are nearly impossible! After a lot of mapping and secret-hunting though, I managed to find a relatively consistent way to win.
I don't show the screen that displays the level I'm on for more than a split second, so I'll list my route here. The color of the cave is a good indicator of this, so that's why I added that as well.
Wave 1 (blue) - Take hidden door to Wave S2 (the warp zone).
Wave S2 (pink) - Take 3rd door down to Wave 7.
Wave 7 (blue) - Find the Special Key (yellow), a normal exit key, enter the mine area, and exit.
Wave 8 (blue again) - Find normal exit key, enter the mine area, and exit.
Wave 9 (gray) - Use the Special Key to open the door and reach the island in the middle of the lava (MAJOR shortcut), kill lava monsters to make a bridge, collect Sankara Stones, and exit.
Wave 10 (blue, gray, then orange) - Use map fragment to find the hidden exit and blast it open. Note that the doors in the level are really confusing without a map! If you're trying this, see my guide on GameFAQs for some help!
Wave 11 (gray) - Nothing fancy. Just reach the top and exit.
Wave 12 (gray with blue sky) - Make your way to the bridge and touch Mola Ram to break the bridge, then climb to the top and touch the girl.
Once you know how to beat Waves 9 and 10, then you can try to optimize other things, such as the number of weapons you collect. In the end though, getting the fastest time requires a bit of luck with the random location of Wave 10's exit. There are 24 possible locations and some are definitely better than others.