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Well first you need to establish the difference in the mileage on either bikes and if the difference is not a lot then continue to read... otherwise go for the one with considerably less miles on the clock.
From 2007 onward a few changes were made to these bikes as follows:
1) Aesthetically, the tank panels, front and rear light cowlings were redesigned and these are not compatible with previous models because on the 2004 the tank panels are mounted on to the edge of the radiator, see 2) whereas the new 2007 are only fixed to the fuel tank.
2) A smaller radiator was introduced.
3) An 02 sensor or Lambda probe was introduced. This can be a pain in the ass when using a power commander or any other fueling devices, such as the Kev Mod which it is sold in this forum by Kev. Because of the 02 sensor, devices such as 02 eliminators came available onto the market to kind of neutralize the effect of this sensor.
4) The best improvement was the introduction of a new redesigned and streamlined swing arm which was only changed on the XTX models and not on the XTR whic we think it's an unfair decision because the old 2004-2005 boxed section swing arm it's quite ugly, also the chain tensioning system is more accurate and easier to work on the new swing arms.
Other than that pretty much everything remains the same. Both bikes are subject to a common (fixable) problem which means they surge and stutter in the low revs, because they are lean and need more fuel in the A/F mix, until you do this:
http://www.xt660.com/showthread.php?...=Co+adjustment
The air box is also slightly sacrificed and therefore a side panel filter such as the DNA Stage 2 makes a great improvement to make the bike "breathe" better and gives you also a nice increase in power and performance.
https://www.e-dnafilters.com/Product.asp?ID=665