The Converter & other P2V applications do handle the hardware change for you. Though it is a best practice to go into device manager and clean up the stale hardware.

This morning I am migrating a Dell GX270 running XP and later a Micron NetFRAME 6200 running 2003 into our virtual environment. I've found the VMware tool to work well for 2000 & 2003, not so good on NT, though this was with the older version of the tool, as for Linux, there is some experimental support but as I am not a Linux person I've not played with it.
The VMware forums are pretty good, some one there might be able to advise you on how to migrate it rather then rebuild it.