That just means the server is configured for Eastern Daylight time, it doesn't affect your site time zone which is set from site settings. The only thing you care about is that the clock on the server is accurate for its own time zone so that times can be adjusted correctly.
So with .NET 4 full trust I would use the Web.fulltrust.config renaming it and putting your machine key in there as I mentioned before.
Then try a smaller upload and verify that NeatUpload is working and that you see the progress bar. If you aren't sure what it should look like try the demo site.
Once you are sure NeatUpload is working, clear the log, then try a larger file, then if it fails check the log again and post one copy of the error here.