Have a look at the posting for TCPIP by Ben, one of the companies has a board using a AVR which drives a IDE HDD, the code is avaliable on the site in c and may help.

I have a IDE HDD working on a 8051 but mine is memory mapped using a couple of buffer and latch chips.

Looking at my code the required sequence to get the drive working is,

issue a reset (toggle the drive reset line)
initialise the drive - check BSY and DRDY bits in the status register, note that DRDY is not valid until BSY=0
verify that the DRQ bit is clear otherwise subsequent register writes are invalid
write 01h to the sector count register
configure the drive/head register as master ie write 0Ah
wait for DRDY bit to show drive ready

enjoy your drive

if you want my code let me know.