My A4000T lacks an "IDE Board," but you have set the jumper to master, tried a known working IDE cable with a known working IDE HDD (also set to master) and used HDToolbox or IDEFix's Find device tool to look for the drive?
Failing this (and the use of the proper KS ROM) I am not sure of any other easy ways to check to see if the port is working. If it is not working, then you can bypass it with a Buddha IDE card (out of production) or an Elbox FastATA 4000 card until you can get it repaired.