What version of MCA do you use?
If it's MCA 6.x to 7.x then Westly's Master Head Pack X is required to install. If you have installed it, but there are missing heads in-game then make sure you activated the esp. Otherwise, no esp activated then missing heads in-game.
I recommend you to install Westly's Master Head X via the Installers tab aka BAIN in Wrye Mash, if you haven't already done that.
AFAIK Better Heads shouldn't conflict with Westly's Master Head Pack X and I'm using both mods without having a single issue for years, but I'm not sure if both Face compilation and World of Faces could cause missing heads.
I suggest that you deactivate both Face compilation and World of Faces then active only one of them and save them separately in a normal save (not quicksave).
Should you still get missing heads in-game then probably both of them are incompatible with Westly's Master Head Pack X. If missing heads are still there then you need to adjust your loadorder by examining the installation order of mods (pluginless replacer or plugin replacer) via BAIN (look for the tiny "Conflict" tab(s) in Wrye Mash.
Remember, some mods comes with a BSA, which needs to be registered in Morrowind.ini to work properly and http://www.theassimilationlab.com/forums/files/file/1059-kingpixs-useful-tools/ is a tool that you need to use for that propose. Also update http://www.gamesas.com/topic/1509142-relz-mlox-anolyze-and-sort-your-load-order/ and doing that could sometimes solve a mod issue.