Your Xbox version doesn't matter for the size of the Bios, the chip holds a 512kb Bios. Sounds like for some strange reason it didn't flash, which in your case consider luck since you used the wrong size bios..You can use the 4981_06 that you are using but use XBTool to resize it to 512kb (or use the X2 5035 like Julius said)
As for flashing, the easiest way is via Network in my opinion, here is the guide:
http://www.team-xecu...shbios/http.htmIf you want to use a disk then this how to make the disk:
http://www.team-xecu...ashbios/dvd.htmAnd this is how to use the disk:
http://www.team-xecu...shbios/disc.htm