Personally, I've never had any problems with FDISK. I know there's an updated version for the version that came with Microsoft Windows 98SE, but if it ain't broke...
Also, I am not sure what you mean by "pulling all the best components" (does this include the mainboard?), but I will assume that you'll be transferring items such as your display adapter and sound card to a new mainboard.
In your case, I would first back up the data you will want to use on your new PC to a CD-R. Alternatively, if you have a secondary HD available, you may wish to copy files from your current HD to this drive instead. (Set it up as the D: drive after you install the OS on the new HD (or E:, F:, G:, ... if you create more than one partition on the primary HD), and from there install any programmes and/or copy documents you need to your primary HD.)
Next, I would wipe my primary HD by running FDISK to remove any current partition(s). Reboot, and run FDISK again to to create a partition(s). Reboot again, and format this drive. If you've done all that, but haven't transferred this drive to your new computer, now would be a good time...
To start off, make sure that you only have the following components installed:
- mainboard
- CPU (don't forget HS&F, Arctic Silver, etc.)
- RAM
- freshly formatted HD
- CD-ROM/DVD-ROM drive
- display adapter
Next, install your OS of choice either by booting from a startup disk, or from the CD directly. (I assume you want to install Windows 98SE/Me, Windows 2000.) After installation is complete, and all settings are correct (resolution, folder options, etc.), it is time to start adding the rest of your components: CD-RW, sound card, modem/nic, etc. After adding a component, start the computer and install the necessary software/drivers. Do not add another component until the previous is completely set up and all drivers have been installed. You'll find it much easier to solve a problem if you do it like this, as you'll at least know what component/software is at fault.
After all has been set up correctly, you can start installing seperate programmes from the CD-R. (If you decided to use a secondary HD for backup, shut down the PC and add it to your system. If you wish to keep using it, set it up as Secondary Master if possible; else, it's fine anyway you prefer, as it'll be removed soon after.)
Next, install your favourite game and frag away...