I'm riding a 2003 yz125, stock main is 410, stock needle is in the 3rd clip, stock pilot is a 40.
Not sure about the '04, but mine wouldn't idle and fouled plugs all the time, and they were oil soaked, i dropped the needle to the second clip and put a 380 main in, and it ran perfectly.
If you're at 6500ft you're at about colorado altitude, when jetting my bikes i always go down 8% on the stock main and drop the needle one clip from stock, and use that as a baseline to start from, sometimes it makes the bike run perfect, other times it requires a lil' fine-tuning from there. Check your owners manual for the stock settings and go from there. just my $.02