Lever Brakeset
Lever Brakeset
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 BR CT91 Shimano Cantilever Brake set  US $7.00
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 SHIMANO DEORE BL M511 V Brake Set FR Levers Mtb Mountain Bike Black V Brake NEW US $9.97
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 SCOTT PEDERSEN SUNTOUR SE BRAKES BRAKESET CANTILEVER US $49.95
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 1 lot 50 Bike Bicycle V Brake Cable Noodle Boots US $18.90
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 6pcs Titanium Ti Bolt Kit for Marta SL Disc Brake M5x16mm 2pcs M6x20mm 4pcs US $18.50
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 Magura Clara Complete Brake Set US $20.50
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 New take off Shimano XT M775 Prebled Mountain Bike Hydraulic Disc Brake Set US $199.99
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 FORMULA SPORT Hydraulic Disc Front Brakeset Brake New US $29.97
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 SHIMANO XTR BR M975 ST M975 Shifter Disc Brakeset NEW US $299.97
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 NEW Avid Code R Hydraulic REAR Disc Brakeset 160mm Grey 1600mm hose US $139.99
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 NEW Avid Elixir CR Hydraulic FRONT Disc Brakeset 203mm Grey Blk 950mm hose US $134.99
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 NEW Avid Elixir CR Hydraulic REAR Disc Brakeset 203mm Grey Blk 1600mm hose US $134.99
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 NEW Avid Elixir R Hydraulic FRONT Disc Brakeset 203mm Grey 950mm hose US $84.99
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 NEW Avid Elixir R Hydraulic REAR Disc Brakeset 203mm Grey 1600mm hose US $84.99
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 NEW Avid XO X0 Hydraulic FRONT Disc Brakeset 160mm Black Red 850mm hose US $169.99
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 NEW Avid XO X0 Hydraulic FRONT Disc Brakeset 185mm Black Red 900mm hose US $169.99
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 NEW Avid XO X0 Hydraulic FRONT Disc Brakeset 203mm Black Red 950mm hose US $169.99
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 NEW Avid XO X0 Hydraulic REAR Disc Brakeset 185mm Black Red 1600mm hose US $169.99
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 NEW Avid XO X0 Hydraulic REAR Disc Brakeset 203mm Black Red 1600mm hose US $169.99
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 AVID BB 5 FRONT REAR DISC BRAKE SET 160MM ROTORS G3 US $49.99
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 Titanium Ti Bolts Kit Elixir Code Juicy Disc Brake 12 Bolts 20 Spacers US $36.50
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 24pcs Hayes Disc Brake Titanium Ti Bolts Kit 12 Rotor 4 Lever 8 Caliper US $42.50
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 2002 Magura Louise FR Front Disc Brake Set with 180mm Rotor US $90.00
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 NEW Avid Elixir 9 Front Rear Complete Brakeset 160mm Rotors Carbon Levers US $260.00
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 Avid Sram XX Rear Disc Brake Brakeset 140mm Carbon MMX US $235.00
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 Avid Sram XX Rear Disc Brake Brakeset 185mm Carbon MMX US $235.00
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 Avid Sram XX Rear Disc Brake Brakeset 160mm Carbon MMX US $235.00
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 Avid Sram XX Front Disc Brake Brakeset 160mm Carbon MMX US $235.00
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 2012 Avid Elixir 1 Hydraulic Disc Brake Set White Front Rear No Reserve US $52.00
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 NEW 2011 AVID XX Front Rear Disc Carbon Lever Brakeset SRAM Brakes US $300.00
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 12 Bolts 20 Spacers Titanium Ti Bolt Kit Elixir Code Juicy Disc Brake Gold US $47.00
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 New Avid Elixir CR brakeset front and rear US $188.02
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 Hayes hfx nine hydraulic disc brakes front and rear carbon lever US $80.00
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 BRAND NEW 2012 Magura MT8 Carbotecture Carbon Disc Brakes Brake SET Front Rear US $549.95
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 Hayes Stroker Ace Front Rear Downhill Bike Disk Brake Set with Extra Pads DH US $51.00
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 2012 Sram XO Avid Elixir XO Complete Brakeset F R New Other NO RESERVE US $250.00
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 Shimano XT Disc Brake Set Levers and Calipers Ready to Ride US $56.00
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 HAYES HFX 9 CARBON BRAKE SET MUDDCUTTER DISCS US $110.00
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 Avid Elixir X0 Hydraulic Disc Brake Set Front and Rear Mountain Bike New Silver US $160.35
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 New avid XO brake set front and rear with 160mm rotors and all hardware US $259.00
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 7800 Dura Ace Brakeset US $10.49
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 HAYES MX1 Front or Rear Mechanical Disc Brake Kit V8 203mm Rotor MX ONE Bicycle US $.01
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 AVID JUICY 35 FRONT 160mm G2 Rotor HYDRAULIC DISC BRAKE KIT Lever Caliper Rotor US $21.50
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 Hayes Nine Rear Right Hydraulic Disc Brakeset Brake Caliper Mountain US $3.25
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 Hayes Nine Front Left Hydraulic Disc Brakeset Brake Caliper Mountain US $16.50
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 MAGURA MARTA SL RED DISC BRAKE SET W ROTORS 6 BOLT 160 MM BRAND NEW CARBON US $420.00
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 SRAM XO X0 HYDRAULIC DISC BRAKE SET NO RESERVE US $100.00
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 2012 Shimano XTR Disc Brake Set BL M988 BR M985 TRAIL US $419.95
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 Avid Elixir R Hydraulic Disc Brake set FR Silver G3 rotor 160mm MTB Bike New US $185.00
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 Tektro Auriga Hydraulic Disc Brake Left Front Lever Caliper Black US $35.00
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How should I upgrade my MTB?
With only about $1,000 to spend, I'd like to upgrade my old entry level MTB, It's a Trek 4300, everything on it is original, 19.5 inch frame.
Front Suspension: RST Gila T8 w/preload, 100mm
Wheel: Bontrager Camino, 32-hole rims w/eyelets, machined sidewalls
Tire: Bontrager Connection Trail, 26x2.0"
Shifter: Shimano EF50, 8 speed
Front Derailleur: Shimano C050
Rear Derailleur: Shimano Alivio
Saddle: Bontrager Select Basic
Headset: VP-A76C-TK, 1 1/8" semi-cartridge, sealed
Brakeset: Tektro V w/Shimano EF50 levers
Just as a heads up, this is actually the info that's on the Trek website, I didn't actually double check to see if mine are the same, seeing how mine is not the 2009 model. Also, I'm looking to hopefully move over to tubeless tires. Thanks a bunch for all suggestions, ideas, thoughts, feelings, and love 
As the others said, you can get a seriously good mountain bike for $1,000.
If you just want to upgrade, I would spent little on it. The first thing should be adding are disc brakes. Mechanical ones will be just fine. Disc brakes in general are a huge improvement over rim brakes.
Go to a bike shop if you want to do this. You want to make sure the brakes mount correctly.