After doing the above, now when my system boots I get a message saying "HFS+ partition error."
So it definitely done something so I looked into it further. After reading many many different problems about booting after DVD installation I noticed that my hard drive seemed partitioned differently. Here is what fdisk shows:
osx86-computer:~ root# fdisk -e /dev/rdisk0
Enter 'help' for information
fdisk: 1> p
Disk: /dev/rdisk0 geometry: 3649/255/63 [58633344 sectors]
Offset: 0 Signature: 0xAA55
Starting Ending
#: id cyl hd sec - cyl hd sec [ start - size]
------------------------------------------------------------------------
*1: AB 0 1 1 - 1023 254 63 [ 63 - 16384] Darwin Boot
2: AF 1023 254 63 - 1023 254 63 [ 16447 - 58616897] HFS+
3: 00 0 0 0 - 0 0 0 [ 0 - 0] unused
4: 00 0 0 0 - 0 0 0 [ 0 - 0] unused
fdisk: 1>
Now I admit i'm a complete noob when it comes to osx and when I originally formatted my hard drive and set it up, I used fdisk auto boothfs command to make the partition. I assumed this was correct as the boothfs made me think the 8MB 1st part. was needed to boot osx.
Looking at other people problems and solutions it appears that you only need 1 hfs partition.
By now though my 10.4.8 is running pretty sweet and I've got it set up just the way I want it so I thought I'd do some more reading to see if I could find a solution. I found a post but I cannot remember where and who was the poster so sorry to whoever it was as I cannot make a thank you reply. I'll try and explain the steps I took as maybe someone will find this information useful too.
First thing I needed to do was flag partition 2 as the boot partition so I booted the DVD installation and ran a terminal. I then typed:
fdisk -e /dev/rdisk0
update
flag 2
write
quit
reboot
This seems to flag the 2nd partition as the boot partition but I assume the bootloader is missing still. (remember I am new to osx and mac stuff so correct me if I am wrong please)
I read that I now needed to copy the boot files from the DVD cd into a folder on the hard drive. So when my system had booted back into osx, I copied all the files from the DVD folder "/usr/standalone/i386/" folder to the exact same folder on the hard drive "/usr/standalone/i386/" some of the files were named boot boot0 boot1h etc.
Now i needed to embed? these files into the boot sector. Well embed is what I gathered from reading different sources. To do this I also needed a file freely available in source form by apple called startupfiletool. After looking around the net I found a compiled version of this and saved it to my USB drive.
Now I came across another problem, i needed to unmount the drive to perform this operation and I needed access to this startupfiletool after the drive was unmounted. Simple I thought, It's on the USB drive so just run it from there. Well I cannot access the USB drive at all from booting the DVD Installation and I have no idea how to add this drive. So instead of messing on trying to gain access to the USB drive I simply burned the file to a blank DVD.
Now this is the final step I took and it worked like a charm. For the following please note -
OSX86inst < refers to the volume name of the installation DVD.
ToolsDVD < refers to the blank DVD I used to copy startupfiletool too.
OSX86 < refers to the volume name of my 2nd partition on the hard drive.
So you will need to replace these with the volume names of your disks.
I booted the system with the installation DVD and ran a terminal. From here I typed (case sensitive):
diskutil unmount disk0s2
cd /volumes/OSX86inst/usr/standalone/i386
dd if=boot1h of=/dev/rdisk0s2 bs=512 count=1
/volumes/ToolsDVD/startupfiletool -v /dev/rdisk0s2 boot
bless -device /dev/disk0s2 -setBoot -verbose
diskutil mount disk0s2
bless -mount /volumes/OSX86/ -setBoot -verbose
reboot
I took the installation DVD out of the drive before I ran the reboot command. I had been using the DVD as a method to boot osx from my hard drive by letting the timer reach 0. Upon Bios screen finishing the next screen was an apple! It was now booting without the DVD !

I'm sorry about the crappy layout of this post but I hope that it helps someone to overcome this problem as it does not seem too uncommon from reading various forums.