not all cf cards can be booted as an hdd, i've seen many problems with that.
For any ssd equivalent technology, you have to find drives with no trim support, because the OS aka win2k or xp can't manage that
What you should have used is called an IDE DOM "IDE disk on module", you have some with the correct male or female 40 amd or 44 pins, they only need an 5vdc to work
they will work like ide drive but having ssd technology / motorless .... and can be fast enough ...
same exist for Sata too, i have a few in industrial pc's, some of them snap directly on the pcb sata connector ... and you still need an 5vdc supply too
if it worked with an ide drive before, you are chasing ghost(s) and don't use what is really needed and may assume an cf card with an ide to cf adapter may work
yes you have the master / slave and the famous cable select modes the cable select mode is tricky, you have some wire twists in it, not all ide cables are identicals,
you have full straight ones too (need the master slave jumper on each drive or hdd cd-rom mix etc ...)
Never had any special problems with win2k setups, but it get finicky with memory problems, when you try to install it it spit some errors, you check everything but the ram sticks have some problems that you did not knew / notice