Can I infer from the tone of your post that you don't believe 99-100%'s exist without mods/cheats? If so, I wholeheartedly agree. I certainly am not one. However, i have played enough to offer some notes.
Scenario 1)
What DryEagle said. I don't mean to sound harsh, but this scenario should never have happened. You had enough scrap for level 2 shields but you did not immediately buy level 2 shields. The only good reason is if you acquired the 50'th scrap in a danger zone which did not allow you to upgrade. You are a sitting duck until you have L2 shields and lots of random things (ex. asteroids) can kill you quick. You have no guarantee you will not see such an event before you get your first 50 scrap, but you can minimise the time you are vulnerable.
Scenario 2)
First Question: Were your weapons manned? If not, this could have saved you by getting your missile charged as fast as the enemy. Most starting missiles are of the fast charging variety, so it is rare for the enemy's to charge before yours if yours are manned.
Second Question: What weapon slot was your missile in? The rightmost weapon powers down first when hit, so put your most important weapon in the leftmost slot. I generally consider missiles more important than lasers. Maybe if your laser had powered down first you could still have missile'd his weapons and stopped the carnage before it got out of hand.
Third Question: Could you see the enemies weapons loadout when you were asked for the tribute? My choice is less driven by if I think I can afford it than by if I think I can win the fight without too much damage. Could you see that he had a missile and a secondary weapon capable of piecing your shield?