I don't know if an IDE splitter would help. It really depends on the nature of the incompatibility, and without knowing you can't be sure. IDE splitters still depend on the devices following the specifications, and CF cards often skip big chunks of the specs as they're normally the only device connected to a bus. But if the problem is purely something like missing master/slave support in the card, it could work.
I have a SCSI setup, I can highly recommend using that instead if you can get your hands on drives or adaptors for reasonable money. I use IDE hard drives attached with 50-pin SCSI to 40-pin IDE adaptors that I bought years ago. They apparently work with CF cards too but they're very expensive these days. Alternatively, you might be lucky and find a CF-SCSI adaptor that you could use if your SCSI board is bootable, or if you don't mind using a microSD instead of CF card,
this kind of device might be interesting...