Bike makers only warranty a product when it was used under the conditions that it was designed for. The 4000 series from Trek is a XC bike, so if they look at your cracked frame and determine that it was from jumpin or playin, they they have the right to refuse a warranty replacement.
So don't get too comfortable with Trek's lifetime warranty. Also, the warranty is only valid to the orginal purchaser of the bike. So if you bought it used, there is no warranty.
Nothing strange there, typical bike industry deal.
As to upgrade, look into a stronger fork or a burlier stem if you are doing some hucking stuff. A shorter stem will make it easier to lift the front the end for jumps are you go into drop. If you dropping on a stock OE fork like a RS Pilot or a Manitou Axel, those things were meant to take abuse outside of XC riding. So it may crack or fail on ya.
Some of the mail order houses have their own housebrands of burly parts for half the price as the big brands.