A new patch was put out today to fix the map size problem.  This unofficial patch mod still works and doesn't break anything (yet).

Edit: BTW, I'm out of town for the rest of the weekend and won't be able to check compatibility for any other patches that come out during that.  I'll check again Monday evening, USA Pacific time.

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.

https://forums.galciv3.com/482848/page/5/#3676392

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) .

https://forums.galciv3.com/482895/page/1/#3676164

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).

Got home earlier than expected.  It appears that the 2.1.30 beta patch released today fixes the problems with Beam and Kinetic miniaturization techs, leaving the Research Institute at 75% instead of 7.5% as the only remaining bug to be fixed.  I will attempt to repackage the mod for that one fix and put the new link in the original post.

Is that the link you meant to post?  For me it loads your own post.

Is the patch not backwards compatible? I am opted into the 2.13 beta, restart game (let it install of course) and go into my game, but those two techs are still 10x as long to get.

Yes, the XML files are loaded when you start a game and then saved into the saved game.  So to see changes in the xml you need to start a new game. 

Unfortunately I won't know until I can download the official patch and compare the xml files.

2.1.31 changed ImprovementDefs.xml, but did not fix the ResearchInstitute, which still gives 75% research.  A new version of my mod is here, containing that fix and only that fix.  Anyone interested in additional fixes and the other changes made by @barrybeal should investigate his files in his post above.  Unfortunately I'm not likely to have much time to do anything further on this until the weekend, if then.