sounds to me like you don't have max transfer set right. it would need to be changed for the cf on ide versus on scsi.
do you have idefix installed?
I have seen cf adapters that do not tolerate 2 ide drives,dont ask me why,even thought they have a master/slave jumper.I dont know if they are wired wrong or what,but half this stuff comes from china.
are you sure the ide cable is good? don't use 80 wire udma cables on standard old amiga 4k ide.
also,you can get right angle molex power adapters that will let the dvd drive fit.If you still lack some room,the chrome fan grill can be removed.. never seen a cd/dvd drive that wouldn't fit with these mods.Plextor drives are super long ;/
adapter cable good for a extra 1/4" :
http://www.xsfans.com/index.php?main_page=product_info&products_id=128oh.. and os4.1 is going to be terrible torture on 2MBs/stock 4k ide.. you really need to use the cyberstorm UWSCSI..
mech