What to do in this situation? Any ideas?

I have a friend, who has a PC running Win98SE and one software he use to do his job at the germans automobile repair shop. This software use an external device called KTS 550 and the software is extremelly delicate to the point of been disable if any, and I mean ANY, changes are made or to the Operating Syst. or to the hardware, and he don’t have a way to replace (reinstall) the software and the data he already gathered from the past use. The PC in this moment has a virus W32.Opaserv.worm, because his Norton Antiv. expirate time ago. He buy new NAV 2003, but I am afraid to install it or use the Symantec’s Removal Tool, once one of the file affected is Win.ini and others system files. I know for other time that if I touch any of this files, the software will become disable.
What can I do, Any suggestions, ideas??
Thanks