There already exists an httpRuntime element in Web.config so uncommenting would create 2 and cause an error. You should just add a longer executionTimeout attribute on the one that is already there.
I would not put NeatUpload settings in applicationHost.config, I would just keep that in web.config. The maxRequestLength on the NeatUpload is for uploads so be careful what you limit that to, maxNormalRequestLength is for limiting non upload requests. You could also remove the maxUploadRate attribute so that upload speed is not throttled.