if the hard disk is partitioned how you'd like, formatted, and bootable,
then you should be able to:
insert workbench disk and type,
copy df0: dh0: all clone.
this will give you a basic system.
for more stuff, (like missing preferences)
insert extras disk and type,
copy df0: dh0: all clone
insert storage disk and type, (monitors and dosdrivers)
copy df0: dh0:storage all clone
insert fonts disk and type,
copy df0: dh0:fonts all clone
insert locale disk and have a look see what the files are, as to where they go. obviously keymaps goto dh0:storage/keymaps etc. (i can't remember what is on here and where it goes) :-D
for day-to-day use. 3.0 is fairy indistinguishable from 3.1 and i certainly had no problems with it for years. can be patched up with TD64, newicons, reaction etc.
for VGA, once you're all installed, drag "VGA only" and a selection of VGA sounding monitors (DBLpal/ntsc, multiscan, super72 etc) out of storage/monitors into devs:monitors and reboot. go into prefs/screenmode, and select one of the new monitors. hit "use". once you find a monitor driver that works with your monitor, hit "save". i hope you have a 23pin to 15pin VGA adapter for the amiga's video port. - but obviously this won't work with games, only workbench launched applications that don't force standard pal/ntsc resolutions.
you'll need a scan doubler for that... :-)
for CDrom, you can attach an IDE device to the IDE cable in the machine. you'll just needs something like AmiCDFS, installed to give you a filesystem in your L: like amiCDFSfilesystem, and device driver in devs:dosdrivers that looks like CD0:
aminet should be able to come up with the goods for CDrom driver software. i think IDEfix97 works fine, but if it is unregistered, it has nag requesters.
sorry i forgot, did you say you had a GVP spectrum28 graphics card in there? should be either a 1 or 2Mb card, fully zorro2/3 sensing, and supported by cybergraphics versions2, 3, and 4, picasso96 and EGS.
i suggest downloading P96/CGX3 (CGX4 is commercial ~£20) aswell to see how good workbench on a graphics card looks :-D