Regarding the Harbor, I think I like it as it is currently. If you want Gold build a Commercial Hub, if you want Production build an Industrial Zone, and if you want Food build a Granary and/or Water Mill. The Harbor is just there to supplement those yields. Since the Shipyard has different yields than the Lighthouse and Seaport, the only change I would suggest is, unlike the other districts, maybe they should make the Shipyard independent from the other two. If you want Production, you shouldn't need to build a Lighthouse first.