Well lets see....There were lots of other changes (some of which might be behind the CtDs), but I wasn't having worldbuilder until these:
I created the Divine 2 promotion (giving Divine the same effects as Channeling2 and Divine 2 as Channeling3),
removed the channeling promotions from priests (giving divine2 to high priests),
removed the Channeling promotion prereqs from priest spells,
made high priest spells require divine2,
made Command require Divine instead of channeling,
fixed a typo in part that was added to CvSpellInterface from Marnok's mod,
replaced all units' PROMOTION_FLYING with PROMOTION_WINGED,
gave a couple more units PROMOTION_WINGED,
added one spell that lets Winged units get the Flying promotion and one that lets them lose it,
I added more TerrainImpassibles and Feature Impossibles to Frost Giants,
allowed Drowns/Muirin/Stygian Guards to enter oceans after Malevolent Designs,
allowed earlier ships to enter oceans after Astronomy ,
gave Wilboman and Frost Giants the Elemental racial promotion,
adjusted the cost, strength, and movement points of a couple of units,
went back to using python for heal (my xml-only approach didn't work, and I hadn't actually touched the python part of Kael's version),
Changed the prereq tech and promotions for Medic 2&3
made Infernal Cities start with Demons Altars instead of Obsidian Gates (I had already made Obsidian Gates temporary buildings from the Dimensional2 spell),
made The Rites of Oghma repeatable,
added the first level promotion of the 4 new spheres to mobius witches' list of possible free promotions,
granted the new sphere's promotions to adepts/mages/archmages (the same way the other spheres are given),
made a couple wonders grant a free mana,
changed Summon animal to a Nature 3 spell,
moved Vitalize to Creation 2 (currently the only creation spell),
made the Train Magic spell (a place holder for until I make Govannon and his students train magic passively) actually grant channeling 1 instead of doing nothing,
lowered the appearance chance of villages and lairs (Marnok's mod had made them way too common)
I made changed the bHasCasted and bIgnoreHasCasted tags for a couple spells, and made one cause war
I think I also deleted portions of some of Marnok's promotions to make them easier to read, since those fields were optional with your schema