Mainly the problem is my main HDD is a 160GB WDC SATA 1 HDD used on a SATA to IDE adapter, however the drive is on-and off detected while mounted in the sled by the CPU but works perfectly fine if laid on top of the CPU heatsink the drive in the front under the ODD prevents the door from closing.
This makes very little sense to me. Are you saying the drive doesn't work when mounted in a vertical position using the bracket?