I have taken your work and found another half dozen errors in specialization tech cost mismatches in MasterTechDefs.XML. There is question why the Synthetic population cap buildings were nerfed in Crusade by reducing the population cap bonus for the these four building but the change is in MasterTechDefs.XML as well as ImprovementsDefs.XML. The higher level synthetic population increase projects are also missing - currently see this post.
The last Starbase factory module in StarbaseModuleDefs.XML is linked to the wrong tech (I believe the tech name and/or proper associated tech for the building was changed in Crusade - there are several other instances of these errors in ImprovementDefs.XML).
You of course still need to mod StarbaseModuleDefs.XML if you want to be able to mix mining bases and economic Starbases and I allow mining bases and cultural modules to coexist as well.
I have made a lot of changes relative to getting the Slaver (Dregnin ) Research Chamber upgrades working (still using Version 2.0 tech names) as referenced in this post) .
The AnomolyDefs.XML needs to modded if you want more tech completion rewards from Artifacts (low percentage) same with Graveyard anomalies being generated more often.
I have played some more with the MapSizeDefs.XML files for larger maps and more max planets and just started increasing the base administrators for the larger maps.
I plan on working on ShipBlueprintsDefs.XML today - supposedly a bunch of ship blueprints have been left out (and previously there were some problems with the 2.0 ship blueprints already (too many drives and not enough life support for many support vessels and concerns with the carrier designs).
Anyhow if you going to continue to update this as an unofficial patch I can post DROPBOX link to a ZIP file of my mod folder for your use in updating your mod.
Currently there is a discrepancy between the leveling bonuses for Research buildings and Factory buildings (0.025 per level for research buildings and 0.01 for factory buildings although not completely consistent - I have also done some minor tweaks to the base bonuses for these buildings but I very much like the increases to the leveling bonuses which can be significant when you can use your adjacency bonuses well).