Much better now!

Ok, so this game is just like Super Star Soldier, but it goes back further than that. I have the original Star Soldier on the NES, and it helps out here as far as knowing the hidden bonuses.
- After the first boss (the large blue ship), Alpha symbols will appear (similar to the "Z"s on SS). They will always be hidden on the far left and the right sides of the screen. When you hear a "clink" sound, keep firing on the side your on and expose and destroy them for a point bonus that starts at 500 and goes all the way to 80000 (the very last one)
- I haven't done it yet, but the orange ring-like boss can be destroyed before it forms for 80000 (just like the "Caesar" enemy on SS)
- Finally, before both bosses, there will be a set of gray metallic round base-like objects. If you can hit and destroy both of them at the same time, you'll get 80000 for that too (just like the green/blue eyes on SS). Note that there are 2 sets before the final boss, the first one set is spread apart a bit wider so you may need to move your ship further back to hit them.
Also, be sure to line up under the missile-spamming enemies just right, so that your front shot is under one row of them and your side shot can get the other row.... tons of points, about 100k per appearance if timed right, you should get about 7 of them to appear per game if you destroy enemy sets fast enough.
When using the exhaust strategy on the final boss, make sure he goes to the bottom of the screen first, then get above him and hit that XF2 button as fast as you can, and make sure to avoid its missiles if they are still on screen when it blows up, you can lose another life.
Extra time and lives remaining equals bonus points, I've been getting around 30 seconds worth and on this game I didn't lose a single life, just enough exhaust.