I have a dual boot system with Slackware 9 and Windows 98. I just re-installed Windows and the only Linux boot disk I have is "Tom's rtbt" but I can't figure out how to redo LILO. Actually I have it on a bootable slackware CD too but it will only run *after* all other install steps have been run - and I don't want to change anything! I can mount my Linux boot partition fine after either boot option, but I don't know what to do next.

run lilo after you have booted.

just running it should work just fine, as previously stated. You might specify the correct lilo.conf though..

Since, when booting with a rescue disc your real system would be mounted. So, lilo -C /mnt/etc/lilo.conf should do the trick.

Also, you can use the slackware install disc to boot your real linux, by specifing the correct root on the boot command line.
Like so, boot: bare.i root=/dev/hda2 (with the correct partition of course).

/Nico