Spice Trade War probably gives a too-large reduction to province peace cost, I remember having 50% warscore and being able to take every province I had occupied and demand release of Hedjaz as well. It would be nice if the CB was extended to affect all Mamluk provinces, or at least some rational subset of them instead of it being 'all their starting provinces except for 5 poor ones in the south'. I would suggest extending it to all Mamluk provinces that are part of the Semitic culture group, that way if they manage to expand a bit you can still conquer them without paying huge infamy cost.
Grain Depot seems exploitative, you can build tons of them eventually and they really boost forcelimits a lot. I had a 300k-man army with 160% discipline, granted I had 3 military NIs but that still seems extreme. On the other hand, without them the quality-quantity slider is laughably balanced, with full quantity being the correct choice in 90% of cases because you simply won't be able to field a modern army with artillery without the assistance of the force limits bonus. I'd suggest copying some of the District Administration code so that there's a limit on how many you can build depending roughly on your country size and adding a scaling cost every time you build a new one. Having 5 or 6 grain depots should be possible if you're large but it should be a significant expense.
Overall the CB and being able to get the 2 arabic cultures as accepted makes conquering the Mamluks totally rewarding in game terms, though due to AE concerns I found that I really didn't have any reason to expand in the Balkans (AE concerns that are amplified by requiring centralisation >-1 for the culture acceptence decisions). Conquering the sunni tribes to the east and north seemed like a much better expenditure of resources, since Hungary is such a poor region ingame and war with them always pulls you into war with Austria/Poland and often Russia, Spain, England or Portugal as well! Persia proved easy to steamroller through and contains some really super provinces with huge tax bases, manpower and/or pepper.
Sending missionaries would have been impossible for me all game even if I wanted to bother with it, I think I had -15% chance in the Balkans between all the penalties there. I had a solid amount of natural spread of the Sunni faith and by 1700 there were Sunni majorities in northern Greece, parts of Georgia, Crete (settled with thousands of Catholics fleeing oppression from Protestants, making the island have a huge population and tons of religious minorities!) and Tebizond which seemed quite reasonable. Shiite minorities in Syria and other regions didn't budge all game; this seems like an unfortunate consequence of making the tolerant/intolerant divide so stark, since it's not possible to be innovative and tolerant of one faith while still suppressing another (which is more or less what happened IRL afaik with regard to shiism in the Ottoman Empire). If I was able I would have 'forced shiites to convert' but it was greyed out all game, not sure if that was due to my policies or just the fact that I never had any missionaries.