Google can follow JavaScript links, unless you are very good at hiding them.

I would not worry too much about the duplicate content, don't expect the duplicates to rank, but your not likely to be penalized for them. you can use a canonical tag to point all search results back to the one page.

I would not no index any pages, any links pointed to a no-index page are pouring their link juice away. if you want to no index a page use the meta tag no-index,follow, this way the search engine will follow the links and flow back out to your site

read about page rank and how link juice flows

http://thatsit.com.au/seo/tutorials/a-simple-explanation-of-pagerank

Are they identical, you say the search equivalent, I just wouldn't treat search engines any different

I remember tests being done in the past and title tag in a link does not pass relevance to the linked page, but it could possible add relevance to the linking page

to make that clear, image page A has this link

dogs

Then page B may rank for dogs even if the page has no mention of dogs because the link text has passed relevance, but I will not do the same for cats.

But if page B was about cats, then it may be possible that search engines see this link coming from a relevant page because of the title attribute. Probably not, but posible

no I don't think so, you would be cleaning up their index for them.

My guess is the large number of 404's was wasting your link juice(100%), also you will lose something from all the 301's (approx 15%),

as for the source code changing I would not worry about change itself. as long as the code has no problems. It a change in content that is the concern.

some other points,

2 weeks is not a long time for things to sort themselves out with this many pages.

You don't need to 301 redirect all the pages, just the ones that had external links.

Also just for interest, Bing treats a 302(temp) that has been in place for a long time as a 301, likewise a 301(permanent) that keeps changing is treated as a 302. Maybe google does the same, I don't know.

I would fix all the 404s and wait

1. unless you have a big thin content problem there is no gain

2. completely reversible, just remove and wait

3. you will have to decide, you seem like you are on the right track.

4. Question you should have asked, is there any downside to no-indexing these pages, Answer Yes there is, all links pointing to a no-indexed page will leak all their link juice, noindex is a last resort, I have never used.

if you must noindex a page, do it with a meta no-index,follow tag, note that was "follow", not "no-follow", then your link juice will flow into the page and back out again.

why are they redirecting back to home page? do you redirect them or are you still infected?

I would make sure they 404

These pages may have links from other spam sites, you don't want them to return a 200.
You want them to 404, in joomla you can make the site use htaccess or not, make sure it dose and 404 the pages there.

That means no body clicks on them, but how did google find them? This is not evidence there is no links, just that no one has visited your site thought them