Hi yes I have 4xEIDE99 same as you with have you read the HD setup part in the readme on the disk cos there is a set procedure for adding a second disk.
Also regarding the devs folder you would prob have a CD0, PIPE, CCO ect but the EIDE99 software automatically configures Hard drives so long as you have setup correctly on the Hardware but will crash if not
regarding the SSequ if you open up ED and check the EIDE99 is at the top of the startup-sequence which is correct, and as you prob already know you wont be able to run the 4xEIDEprefs if there is other software collidiing with it like. eg IDEfix,Also have you tried it without the ACA tune maprom lines removed?
Also where is the{ sys:Prefs/4ExIDEprefs} in your SS ? its in mine
And also I lost count of the number of times I had non booting probs, and all it was is the Adapter on the adapter IDE pins/port not seated down correctly, bad design:(