I really cannot help you with the increased incidence of CTDs when using my micro-mod. I, for instance, have more than 20 hours of gameplay, more than 100 turns and dozens of battles (many of them trigerring my spoils) and not a single CTD yet. (and I am using BI.exe and few other mods and my personal tweaks on top of that)...
As for the size you use: my mod makes the unit-sizes visible as the game perceives them. I.e. every general should have a trait saying "Huge/Large/Norma/Small Unit Size" if it corresponds to your actual settings, everything should be just fine. If not, apply the fix (see my post above) over my micro-mod and start a new campaign. If it still wrong, it means that the fix is still not complete, so please report that as described in my previous post.
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