I just checked W98se (that is Second Edition, which you seem to want to call v2), the selection of Add/Remove Programs, Microsoft Internet Explorer, and clicking on [Add/Remove] comes up with 3 selections:
- Add a component
- Repair Internet Explorer
- Restore the previous Windows configuration
there is no "re-building"
If you want to correct some possible IE problems, you might take that last selection, to restore the previous configuration, which will take you back to IE v5.5 (or v5 if you had that last).
Then, once you are back at that prior version, just go to the Windows Update website and re-load the latest version of IE, which will be v6.
FYI, The term "re-build" in computerese is typically where a person takes the source code of an application, and re-compiles the code, thus creating new code. There may be other variations of that same term, as well, but re-building is not what you do when installing, or re-installing, or repairing Internet Explorer.