Welcome to the joys of DOS memory management. It's not the physical memory but how it's set up. All down to original PC XT having a 640K memory limit, so you have to tell the computer what to do with any memory above this to maintain DOS compatibility. Windows NT/2000/XP onwards don't have this problem. Have a look on the phils computer lab website and it should tell you how to set up your config.sys and autoexect.bat files to fix this error.

What does "mem" say?

Make sure either HIMEM.SYS is loaded in config.sys or XMSMMGR.EXE executed via autoexec.bat or directly in the DOS shell.

You haven't mentioned what version of Windows You are installing, If not already I would only use Win95 on a 486.
Just load Himem.sys in your config.sys file and I reckon that should sort it out. It should look something like this.

DEVICE=C:\DOS\HIMEM.SYS

Load it first in the config.sys

PCI READ CONFIGURATION FAILURE is most probably reported by scsi driver that tries to scan PCI for a card but there is no PCI in your system - that is totally fine. This happens when you boot from Windows 9x boot floppy.
The thing that's strange is the extended/expanded mem error however. Windows 9x boot floppy loads HIMEM.SYS that manages XMS, so this is a weird error.
Try editing CONFIG.SYS and adding /TESTMEM:ON /VERBOSE flags to HIMEM.SYS. It may explain you why it doesn't load.

Also, there is /MACHINE: flag for HIMEM that you may need to set po ps2 since you have IBM PS mobo:

/MACHINE:xxxx
Specifies what type of computer you are using. Usually, HIMEM can detect
your computer type successfully; however, there are a few computers that
HIMEM cannot detect. On such systems, HIMEM uses the default system type
(IBM AT or compatible). You might need to include the /MACHINE option if
your computer is a type that HIMEM cannot detect and if HIMEM does not
work properly on your system by using the default system type.

Currently, systems that require this option include Acer 1100, Wyse, and
IBM 7552.

The value for xxxx can be any of the codes or their equivalent numbers
listed in the following table.

Code Number Computer type
---------------------------------------------------------------------------

at 1 IBM AT or 100% compatible

ps2 2 IBM PS/2

ptlcascade 3 Phoenix Cascade BIOS

hpvectra 4 HP Vectra (A & A+)

att6300plus 5 AT&T 6300 Plus

acer1100 6 Acer 1100

toshiba 7 Toshiba 1600 & 1200XE

wyse 8 Wyse 12.5 Mhz 286

tulip 9 Tulip SX

zenith 10 Zenith ZBIOS

at1 11 IBM PC/AT (alternative delay)

at2 12 IBM PC/AT (alternative delay)

css 12 CSS Labs

at3 13 IBM PC/AT (alternative delay)

philips 13 Philips

fasthp 14 HP Vectra

ibm7552 15 IBM 7552 Industrial Computer

bullmicral 16 Bull Micral 60

dell 17 Dell XBIOS

Something else weird in that config, unless you're intentionally slugging it, CPU cache is disabled - is the CMOS battery good?

Thanks for the replies. I am trying to install windows 98, i know this is not ideal for a 486 machine however the idea of this is to recreate my first computer i had as a kid as best as i can. On that machine i had upgraded it to windows 98. My childhood memory was that it wasn't really any different speed wise to 95 but i expect it wont run great on a 486. I'm currently using the windows 98 boot floppy to install windows 98 with cd rom support. I will have to do some reading on the suggestions to get my head around them as this is all new to me. I assume the config.sys and himem.sys should be on the boot floppy and can be edited prior to installation.

Also regarding cpu cache, the cmos battery was flat so it kept defaulting to disabled. Fortunately its just a 3v lithium cell on this board so i replaced it and set it to enabled.