Just copying over the json file wasn't enough. My problem was that I started the client before copying the blockchain and hosted data back over. Actually it was copying while I started the new client the first time.
I would recommend making sure you copy EVERYTHING first. Json file, blockchain, and hosted stuff prior to ever starting the new client.,
I'm guessing that it's possible, though I don't think we'd be willing to distribute a completely different set of binaries with the GPU disabled. If you are a developer and comfortable monkeying around a bit, the source code is here: https://github.com/NebulousLabs/Sia-UI
If you do end up making your own release process so that you can disable the GPU, please share it with us. We'd like to put it on our website.