I'm using a IBM 2 GB drive in my GVP HD8+ without any problems. It can be accessed without any problems from HDInstTools, HDToolbox and the GVP FaaastPrep program.
IIRC I had to softkick to Kickstart 2.0 in order to load up the HDInstTools program to setup the drive (FaaastPrep and HDToolbox reportet errors under Kickstart 1.3).
What version of the GVP rom do you have? I was once told that the older versions of the GVP rom had issues with larger harddrive. You should be fine if the rom is ver. 4.15 or higher, but not really sure on this one.
As for the JP2 jumper, I'll try to see if I have the manual somewhere.
-EDIT-
Read the first post again, and saw that it answer to my question. Try to remove the jumpers from the ID pins, it should make the drive unit 0. Then a jumper on the SCSI term pins, and you should be set to go.
You specify the right driver when launching HDInstTools right? The program should be started from CLI/Shell with gvpsci.device as a parameter.