Long story short, I had the bug where Windstad manor was invisible after crafting the small home. I disable some mods that may have caused the issue (probably Distant Detail). I go back to Windstad and try to craft the main hall and fish hatchery. This time they all show up! However, the "entryway" is bugged and I cannot get into the house. I can walk right through it, essentially.

I have no saves to revert to before building the small home. Is there a fix for this on the PC? I have the UHFP installed, but that obviously didn't prevent this. The main thing I wanted windstad for was the fishery, which I was able to build. The fish should still spawn even if there is only a shell of a house there, right? As long as the fishery works, I'm happy (enough)

Sounds like you're having a mod issue and you would have a better chance to solve it in the http://www.gamesas.com/forum/183-skyrim-mods/ forum.

Please post your loadorder.