Hallo rsad_rao! I'll do my best to help you with your problem though I'm pretty much a Linux newbie myself.But that's what this forum section is all about,I suppose.
That said,let's go on to your problem.First off I can tell you that yes,your Windows 98 installation is gone.What you did during your Linux installation,when you skipped creating a swap partition,was to create a single Linux partition across the entire second hard drive (or logical drive),and that won't work.
What you need to do first of all is to reformat your D: drive with Disk Druid during the Linux installation.Look for any Linux partition,it should show up automatically.If it doesn,you have to delete it manually,in order to be able top set up a proper set of partitions to host your Linux distribution.
Is your D: (in Windows) a separate physical hd or a extended partition&logical drive?
If it's a separate physical hd,the current non-operable Linux partition probably resides on hdb1.If D: is an extended partition&logical drive on your first physical hd,the non-operable Linux partition probably resides on partition hda2,whereas hda is the first physical hd and hda1 is the first partition on that hd,hda2 is the second and so on.The second physical hd is hdb and the first partition on that drive is hdb1 and so on...
With that crash course in the Linux partition system out of the way,let's move on.As I wrote,you need to create a proper set of partitions with Disk Druid,to host your Linux distribution.During installation,create a Linux swap partition that's about twice the size of your amount of RAM,and a Linux native partition that covers up the rest of the drive and mount it at the root (/).If you want to,you can create two Linux native partitions and mount the second as a separate folder for example (/varfiles).That way you won't lose the files in that folder&partition even if you have to make a complete reinstall of the Linux distribution.
I think that's all you need to know to prepare the installation of your Linux system.If you run into more problems,just drop me a message.
Also,if possible,install Lilo in the MBR of hda.