Hi Robert,
You might try increasing the maxNormalRequestLength, but other than that NeatUpload is only for uploads, not for downloads.
I'd also look at the executionTimeout setting on the <httpRuntime element.
Downloads may be handled in different ways, features like the Shared Files feature will write files into the response, whereas if you are downloading files directly from the file system by url, the download request will be handled directly by IIS. So knowing what files you are downloading and how would be helpful.
I'm about to get on the road and will be traveling most of the day so will be offline, but I would look for any clues such as errors in the mojoportal system log that correspond with the failed downloads.
Best,
Joe