So I went back to familiar old fdisk to do the partition. This seemed to let me complete the installation with less hassle than I normally expect from Linux. I reboot and get a screen that says "LI" (i.e. it halts partway through the LILO boot process). I try booting from the rescue floppy I created during installation. Same result. I go back to the cdrom which had easily booted the installation program. Same result. Looking through the Sony manual, I find that I should be able to reach a bios menu by pressing F2 when the Sony logo comes up during the boot process. I note I get to the "LI" screen without seeing any Sony logo, and F2 does nothing. I get desperate enough to send email to Sony tech support (it's 5 days later as I write this, and the only response has been an automated acknowledgement that my email was received).
As I try to sleep on the problem, I wonder how anyone could design a system that would switch without warning from booting off the cdrom if present to ignoring it. The answer that comes to mind is that resuming operations after a notebook's power management feature is activated is a lot like booting, but one wouldn't want it to check a cdrom. I conclude the system is trying to resume operations by restarting Linux as if it had been suspended. After a fair amount of time and despair, I eventually stumble upon something in the Sony manual which tells me to hold the power key down for 4 seconds to convince it to go through the normal boot process. Now I can finally boot from the installation cdrom, or from the floppy. I can use Linux from the hard disk ok when it has the floppy to start the boot process, but that isn't an acceptable long-term solution, because I plan to put a second battery where the floppy currently is. Also, Windows won't boot even when I use fdisk to make it the boot partition again.
At some point during that process, I had seen a report that Linux sometimes had trouble booting from cylinders above 1024. Newer versions of LILO have better support for this, so I installed the latest version. No change. I conclude that I should try shrinking the Windows partition. I probably should have done that in the first place, since it's hard to imagine that there's enough good Windows software to fill 11 gigs.
I end up doing a full reinstallation of the original Windows software from the cdrom's that Sony provided for that purpose, and then using fips to shrink the Windows partition to about 2 gigs (fairly straightforward but hardly quick processes). I am now able to reinstall Linux and boot it from the hard disk.
setpci -s 0:7.2 command=0
But some graphics problems remained. Fungimol wouldn't start, complaining that it couldn't find a display with at least 15 bit color, and RasMol acted really wierd - I had to compile it for eight bit displays, and moving the cursor in and out of its window caused semi-random changes in the colors of the whole screen.
After wandering around the net a while, I found some advice at LinuxPlanet - Print - Leading and Bleeding with XFree86 4.0 and KDE 2 Beta, and modified the generic Device and Screen sections of the XF86Config to:
Section "Device"
Identifier "ATI Mach64 GT (264GT), aka 3D RAGE"
Driver "ati"
VideoRam 8192
EndSection
Section "Screen"
Identifier "Screen0"
Device "ATI Mach64 GT (264GT), aka 3D RAGE"
Monitor "Monitor0"
DefaultDepth 24
Subsection "Display"
Depth 24
Modes "1280x1024"
ViewPort 0 0
EndSubsection
EndSection
Now the graphics seems quite nice. The 1280x1024 might not be the best
resolution it can handle at 24 bits, but it's impressive enough that I'm
in no hurry to fiddle more.