In response to post!
1) For the timers the real question is how often do you want players to check in with the kingdom? Assuming 1-2 hrs is roughly the edge point, you probably want to increase generation per tick (or have it stock up over time), and then have the timers be a decrease every 10 mins or so.
2) Production speed needs to be automated and in the back ground, link it to something akin to what the gold every x amount of time was previously. The cap per resource is fine, but many intermediaries should be removed, unless the base resources are going to automatically convert as they did in the previous turn based iteration. Any researches or requirements to the final product can have longer timers if needed, but intermediaries are silly and are extra micromanagement no one want to deal with in a rpg focused game.
3) Re-iterating, the max storage limit is definitely over kill.
4) see 3
5) See 2. The intermediate products really have no purpose here unless they are automated- even in a game about making products and selling them (offworld trading company!), there are few-no intermediaries. It's all raw resources-> product.
6) That check would be a good idea I think, increase the base resource cost to do the research/make the product, and then once it's been made at least once, set off a flag confirming the item is there and no longer need to make it.
Battle system skills: Given that the game and combat was clearable prior to these battle system skills being added, it's hard to say what would be needed to make reputation valuable. That said, I haven't tried these at all yet given that the initial attempt of trying to get kingdom building to work went... poorly, so I can't give accurate feed back here.