Ok the first thing I noticed in the boot was that usb appeared to be loading but kept giving irq error messages with a message saying to check the bios settings. So looking at Advanced -> USB Features there was only one option which was to enable the USB floppy. It was enabled so I disabled it. Looking at the PCI Configurations and there was only one option which was IRQ Reservation. It listed IRQs 3,4,5,7,9,10,11 as available. These were all reserved for use by legacy ISA devices. Didn't worry about doing anything here yet, so I saved the settings and then continued with the boot.

Ok noticed the same errors including also hdc: IRQ probe failed. Looking at

   $ dmesg |less

and the first thing of interest I notice is
ALI15X3: detected chipset, but driver not compiled in!

so time to have a look at the kernel configure file to see what options have been compiled in.

Ok looking at the config file I see that the ALI15X3 is a block device option and it is not set.
So I run make xconfig to check to see what other options need to be enabled to get it to work.
It is in the IDE chipset support/bugfixes section in the config file and I found it in the IDE, ATA and ATAPI Block Devices Section and is called ALI M15x3 and the output of the command "lspci" shows that the ISA bridge is an ALi M1533 PCI to ISA bridge so that looks right. It looks like no other options need to be enabled to get it to work so I just selected yes for it to be compiled into the kernel.

Also I added APM as a module as it is currently not available and it might be useful given some of the issues that are happening with ACPI.

Ok exited make xconfig and then installed kernel-package to build a deb of the kernel and kernel compiling a bit easier.

   $ sudo apt-get install kernel-package
   $ sudo make-kpkg clean
   $ sudo make-kpkg --append-to-version new kernel_image

After a bit of time the make commands stop appearing on the screen so then
   $ cd ../
   $ sudo dpkg -i kernel-image....deb

I said no to creating a boot floppy
Yes to installing a boot block using the existing lilo configuration and that was it the installation was successful.

Now before rebooting first checked to see that lilo still had an option to boot from the previous kernel so I wouldn't be stuck if the new kernel failed.
ls -l / shows that the current kernel is linked to bzImage while the new kernel is linked to vmlinuz. Just a quick check of the lilo.conf file and we should be away. Ok the bzImage is set as the default so I will change that to Linux therefore making the new kernel the default.

   $ sudo lilo
   $ sudo reboot

Big problem still get the message

PCI: No IRQ known for interrupt pin A of device 00:0f.0. Please try using pci=biosirq.

and then at the line

ALI5x3: not 100% native mode: will probe irqs later

it hangs.
I will try restarting and passing the pci=irq option to the kernel at boot time.

Ok did that but still got the No IRQ known message but it didn't offer the pci= advice however it still hung after that line.
Will reboot and try passing the pci=biosirq to the old kerenl and see what happens.
Still getting the same error messages.