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LINUX, WINDOWS AND PARTITIONING WOES

When I got my new hard disk installed from the vendor, they had installed Windows 98 (yes I still use it with pleasure - no problemo) from my HP Recovery CDs on it.
The Seagate HDD - 40GB was split into :

C: 10GB and
D: 30GB

So I wanted to install RedHat (PCQ) 8.0 Linux from the PCQuest CDs.
I used fips.exe (it comes with all Linux CDs in a folder named dosutils) from DOS command mode to split the active partition ie C: to something like 5GB (initially fips.exe gave some error like last sector not free and a 'bye cannot split partition')
Then I defragmented Windows (with Diskeeper Lite - stupid piece of software was an evaluation version and allows defragmentation only once but its fast) and tried fips again and it partitioned the disk and I installed the complete Linux system.
It was then that the trouble started - Windows became unstable and crashed and became frozen or slow at times meaning frequently.
I defragmented Windows again and guess what after that I had a premonition that something was wrong with the Linux part and after I pass the GRUB OS loader screen and some initializations I am bang on target. The OS doesnt find a series of files and throws me into a shell to login and neither X Windows starts nor anything else - I am like bugged and havent installed Linux again, yet. Can I recover the Linux install from this mess - I doubt but a reinstall will I am sure hive the same hassles again!
What is the basic problem - comments are welcome . . .
Was my partitioning process flawed? As this has happened earlier too on my crashed harddisk . . .
What other options (Ranish partition manager does not support large disk sizes I guess) are present to split a disk which has only Windows on it (all over it;-)) ?

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