I swapped the alloy fork on my old Fuji Absolute for a carbon fork and was pleased with the results. Problem is,on your bike you'll need a fork that has V brake mounts,which means a road fork is out. You'll need a cross/hybrid/29er fork,which will be expensive.
Two better options are a steel fork or lower psi tires. Steel forks are cheap,you can get a nice one for under $75. An even cheaper solution is to go with lower pressure tires. I think your Bontragers are like 100-120psi? Try some tires that are around 80-90psi.
BTW,you are trying to avoid the potholes,right? I'm always amazed when I see people just bomb through them.
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C'dale BBU('05 and '09)/Super Six/Hooligan8and 3,Kona Dew Deluxe,Novara Buzz/Safari,Surly Big Dummy,Marin Pt Reyes,Giant Defy 1,Schwinn DBX SuperSport,Dahon Speed Pro TT,Brompton S6L/S2E-X