only problem with getting a used bike for cheaper is that it has had the shit canned out of it for 6 years.
bushes and bearings will all need replacing: swing arm bushes, bearings and seals, wheel bearings, head stock bearings, etc
full engine rebuild: piston, rod, bearings, seals, gaskets, oil, coolant
new pipe if its damaged
re pack the silencer
new air filter
new tires
potentially new discs and pads and brake fluid
2500 for a second hand bike plus a 1500+ for the above (parts only), so that $4600 brand new 06 yz is seeming rather cheap.