Well i have tried every possible combination with various different results from just have 1 HD, 2HD, no Roms, 1 Rom, 2 Roms LOL. Even at one point told me i had an invalid system disk and put in a new one (so i used Go-Back to revert back to earlier).
Well i now have it set is:

IDE1 MB - old HD (master) - new HD (slave)
IDE2 MB - CD/RW (cable select) - DVD/RW (cable select)

Have to admit i am lost. System is running (well doesn't appear to be freezing now) BUT the disk still spins (or does something anyway lol) every now and again.

I have not tried to use either ROM drive though. Just wait and see i guess, but i presume the CD/RW one will give the problem if i try.