Just uploaded v1.3. It fixes a freeze involving antelopes, makes the game run faster and improves the pathfinding. Hope that fixes the lag.
The stonemason might have not been picking up stones because they were reserved by builders on their way to pick them up. As for the windmill, I'm not sure what the problem might be. The new patch does improve pathfinding again so might just fix the issue. Would help if you could send your savefile so I could have a look at what's happening!
Edit: 1.3.1 also optimizes roads: if you had a lot of those, this new build will probably make the game a lot faster!