nearly 2 operating systems on one disk

My hard disk with Win98 has been accidentally overwritten with the start of NTserver. Now my machine boots to the the screen where you choose the operating system. NT does not boot, as it is not properly installed.
However if i start the boot process choose win98 and let that start to boot (it never finishes booting, then recycle the power I can boot into Win98 safe mode.
Any ideas how I can remove this unwanted version of NTserver without completely reloading my system. i.e. which filesneed deleting ect

Thanks in anticipation