"is there a way to control the Amiga workbench pointer with the usb keyboard?"
Yes, should. Command keys such as this are remapped, and normally work.
"Also, was there any way to do a warm reset through a usb keyboard?"
Again, yes. This should work.
"I cannot seem to find the combination with a usb keyboard (my usb keyboard is connected to an Amiga 2000 / os3.9 / highway)."
I was using the windows key I believe as the Amiga keys...
Last I used USB keyboard and mouse was through subway and Poseidon on a A1200. It work great. You could not however enter the early boot up menu, as the drivers were not load at that point.
Some better help may be on the way....
:-)