Greetings,
I believe I have found a problem with the Imperial Reconquest system. I was surprised when I controlled all of Sicily, Serbia, Croatia, Bulgaria, Byzantium, Coloneia, Mesopotamia, Edessa, but could not start a war to reconquer Cairo or Tunisia (which I should be able to, according to your map on the first post.)
After checking your codes, the problem seems to be this: as I started with the "Manuel Komnenos" bookmark, much of Tripolitania, Tunisia and Egypt has drifted out of their original kingdoms (North Africa into Mauretania and Egypt into some titular sultanate) after a century. The codes for Imperial Reconquest targets de jure territories of specific kingdoms, however, so any territory that drifted out of them would become unavailable for reconquest.
Is this working as intended? The reconquests are based on the claims of ancient Rome, so it seems proper that they should hold no matter the current de jure kingdom covering those lands.
PS: And Genoa drifted out of Italy and into Genoa - I spend half an hour wondering whether that tier of Imperial Reconquest on your map actually covers Genoa or not when I realized I could attack Venice, Lombardy or Susa, but not Genoa.