The ECU in the 04 bikes was indeed one of the "troublesome" ones. As well as the TPS was recalled in all the bikes from 2004 to 2005 included.

My friend you need to get on to Kev (obviously after you've joined the XT Supporters) because his help is much needed in this case, the 2004 bikes were a bit of a dark horse, and you need Kev's help to get your bike to work fine, but in the meantime I suggest you increase the tickover (idleing speed) to at least 1450-1500rpm to ensure that on close throttle the bike doesn't starve of fuel and cut out.