Yes the 2006 and newer are totally different Machines. Stock vs stock the 04 and 05's make 32HP and the 06+ make 38HP from factory.
Your 2013 has wider bore, shorter stroke, the head design flows a lot better then the stock 05, the Carb on the 06+ have FCR style Carburetors (unlike the butterfly style that the 04 and 05 used) the 06+ also have a 12:1 Compression ratio vs the 05 only has 10:1 , Also the 2006 + also revs 500 RPM's more then the 05 does.
I believe the 2006 to 2014 TRX450ER/R are identical... other then I think that in 2008 they changed the Cam Shaft, Air box and head light, and then 2012 i think they went to the White plastics and Metallic Orange frame. Other then that the engine was mostly un touched.
I do agree I like the 05 better on trails. My sisters quad is a 2006 and mine is an 05 "06 is pretty much identical to the 2013) and I noticed her raps out and runs out of gearing really quickly, which is not bad.
Honda redesigned the TRX450r and ER in 2006 to be more competitive with the YFZ450.
The 06 and Up are nice though because they are/were Maybe stil are $ 3000 or $4000 cheaper then the YFZ450 and with about 1500 bucks in mods for the TRX450ER you will walk all over other 450's.
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