Bug report
I've reached the Modern period in my game with the previous update (standard speed, no autoplay)... no crashes thus far, with city ownership changes happening normally. That goes for occupation, as well as returns and gifts via diplomacy. Save and load causes no apparent issues.
In a prior game, with the older update (the one with the housing yields, but not the TEST_REQ buildings) I ran into a crash where I attempted to capture a city (capital) which had 2 previous owners. I noticed the city wasn't selectable for transfer via diplomacy, and in the tuner it showed the
valid flag set to 'false'. I haven't been able to recreate that scenario in my current game... very AI and map dependent... but I'll keep looking to do so.
In both games, city population became globally stuck around 6. Growth pretty much flatlined, despite having full stores of food with housing at the maximum level (none left to build). No nearby armies or combat pulling food. This is true for myself and all AI players. I'm guessing this needs adjustment after your recent revamp.
No other obvious problems or log errors.
-----
Gameplay feedback
On combat...it's playing relatively well. I've had numerous scenarios with extended border battles where I needed to replace depleted units and tune nearby cities so they provide adequate supply (rush build herbalist or blacksmith; increase local food supply; etc). This is a fun element. The AI seems to do reasonably well, despite being naive to the system. At least, that's true when combat occurs within supply range... so it defends well enough. It also manages to capture cities if they're close enough, or it has an abundance of units. Of course, the usual (mildly ********) army operations will sometimes break otherwise good performance. Such as where a unit will simply play dead, or a bunch of embarked melee units try to surround a ship... vanilla things

. AI players do, however, typically make good moves that are accentuated by the limited stacking allowance. Ranged units are frequently protected with stacked melee, which works well with the AI tendency to swap out low health units. I also think the extended combat time afforded by continuous "healing" from reserves and supply covers many tactical mistakes, at least in the short term. It does seem to lead to sustained aggression early to mid combat, while reserves are high.
Overall, combat is much more entertaining in this configuration... sound tactical maneuvering is more important, and you have to keep an eye on how it's affecting city development. And weak city development will affect local combat. Good stuff.
On housing... I know the model is very basic at the moment, so not much to say... other than constantly upgrading housing is extremely tedious

. I don't know that it needs to be quite so granular, and what you had mentioned about city expansions (i.e. re-purposed, adjacent districts) sounds like a good way to go. Perhaps, instead of deliberately building specific classes of housing, population stratification could be accomplished strictly by "needs fulfilled"
On research... will give the ideas you outlined some thought and read the linked discussion. I've always favored the idea of less deterministic research outcomes. You should certainly be able to nudge things in a particular direction, steer the ship towards a long range goal. But turn-to-turn behavior, along with external factors, should impact progress, sometimes unexpectedly. I think the vanilla eureka concept suffers from absolute predictability, but was nonetheless a step in the right direction.
Do you plan to do cultural migration this time around? Similar to the Revolutions component of the RED project, you could have relevant ideas (research points) diffuse via the same system that spreads cultural unrest. That's more interesting than generic diffusion, since it's proximity based. Even better with trade routes allowing deliberate "pull" alongside what you get naturally from proximity or conquest.