iframe is a valid tag, and it is possible to use a Javascript to create an iframe when the upload button is clicked. (I haven't tried it yet... will do later.)
The vars are hardcoded into HFS, I have no control over them. (You will have to ask rejetto for that.) (HFS-vars are linked in sections so I think it may be somewhat time consuming to do.)
The refresh rate for the progress is specified in the HTML page, currently I do not know a way to change this unless some other script is used. (Don't know of any, however.) You could use Proxomitron to change this value, however.
The BitTorrent protocol differs the HTTP protocol so unless you are only serving .torrent files, you will have to somewhat rewrite the program and implement the BitTorrent protocol.