Elwood:
With large fastq files your best option will be either using public server (which is having difficulties today) or running a local instance of Galaxy. We are very much aware that the public site is not behaving well. It will be back on-line today and in the coming weeks we will be switching underlying infrastructure brining much needed relief to all Galaxy users at once.
The best venue for posting such questions is out galaxy-user mailing list (I CC'ed it here).
Thank you and sorry for the main site troubles.
anton