Thanks for the replies. I was, if anything, even more confused concerning the suspicious 'long script' code snippet - I went through and checked every single text based file in the entire site, and that code (or anything like it) does not exist anywhere!
Also though, the problem seems to have gone away, in that Avast no longer flags the site as a problem... I wonder if the issue was actually not in my site and my code was calling some function from somewhere else (JAlbum for example) which had an infection and has dealt with it? Either that, or there was something in the online site that I didn't find, but the re-upload of the clean offline version dealt with it... Anyway, in the absence of a problem, I will leave it for now.
Re. the other recommended fixes - the whole site needs an overhaul and that list gives a really good handle on how to proceed, so thanks for that!
Cheers,
Geoff