If you use:

domain:example.com

then this will disavow www.example.com, example.com and all pages coming from this domain.

Take a look at your organic traffic only.  If you use Google analytics, go to Aquisition --> All Traffic, then choose google/organic.  Can you tell what date the drop happened on or started on?

Now go to Behavior --> Site Content --> Landing pages and click on each of the top pages.  Is there an obvious drop for each page or just the home page?

How old is the site?

Can I ask why you did the 301 from domain.com to domain.com/home.html?  Is there any chance that the /home.html page has either a noindex tag or is blocked by robots.txt?  Is there a canonical tag on the /home.html page?  If so, what does it say?

Absolutely do the disavow first.  There's no reason not to, especially if you are dealing with an algorithmic issue.  (For some sites with manual penalties, I'll submit a disavow as soon as I can and then do the outreach.)

On a side note, if you have an algorithmic issue (i.e. Penguin), no one knows for sure whether you even need to remove links.  Of course, there are benefits to removing links.  Google will tell you to do so because you don't want people to look at your site's links and see bad ones online.  But, I recently asked John Mueller in a hangout whether link removal (as opposed to disavow) was necessary for Penguin and here's what he said:

From a theoretical point of view, using the disavow tool is enough...from a practical point of view it almost always makes sense to still delete those links as much as possible.

You can see the response here at about 41:20: http://www.youtube.com/watch?v=KWYooFjmx5c&list=UUthrUiuJUtFSXBUp48D8bAA&index=2

The main reason why removing may be better than disavowing is because it can take weeks or months for a site on your disavow list to get recrawled and as such be disavowed.  However, I have found that in most cases, if you have spammy links, if you don't control the login info you used for link submission (or if there is no way for you to remove the link yourself) the response rate is always very poor (like 10-15% if you're lucky).

If you've been hit by Penguin, there are two things that need to be in place in order to recover:

1. An EXTREMELY thorough link audit and disavow.  IMO it's not enough to get 80-90% of the bad links.  The only sites I have seen recover had close to 100% disavowed.  This means doing a manual review of every single domain linking to you from every source you can find.

2. A site that has a base of good natural links with the ability to attract new links.  If you don't have that and you are planning on manufacturing your own links again then you probably will not recover.

Does your analytics data go back as October 3?  If the drop happened October 4, then I would indeed be worried about Penguin.

Have you been building links to this page?  More specifically, have you built keyword rich anchors to this page?

Do you see any manual spam actions in webmaster tools? (WMT --> Search Traffic --> Manual Actions)

I can't see this causing you problems.  I've commonly noindexed huge numbers of pages, mostly for sites with Panda issues, and in several cases we've seen great increases in traffic with a future Panda refresh.

It's not possible to remove a Penguin issue in 3 days even if you have managed to get Google to crawl and disavow all of the links on your disavow file.  This is because you won't be able to escape Penguin until Google refreshes the Penguin algorithm.  AND...in order to see a dramatic recovery like the Link Detox graph shows, you'd have to have a site that has a really good base of good links underneath the low quality links.  Most sites with Penguin issues will not see a dramatic recovery...and if they do, again, it would almost always be on the date of a Penguin refresh.

However, the Link Detox tool is describing a manual penalty, not Penguin.  (However, they're a bit misleading saying it "speeds up recovery from a Google Penalty".  Officially Google will tell you that Penguin is not a penalty, but simply an algorithmic change, but most webmasters would tell you that Penguin is a penalty.)

If it's a manual penalty, then you don't need to have the links in your disavow file crawled in order to lift your penalty and if this is the case then the "boost" that they are talking about won't really help get a penalty lifted. Within 24 hours of filing your disavow, the webspam team is able to see what is in the file.  When they review your request for reconsideration, they check to see if you have disavowed the right links.  It doesn't matter if those links have not been visited and thus disavowed yet.

Is it possible to lift a manual penalty in 3 days like Link Detox's website suggests?  Yes.  I've had it done.  We once filed for reconsideration and three days later we had a response saying that our penalty was revoked.  But, out of the hundreds of requests that I have filed, I've only ever once had Google respond that quickly.  Most requests are taking 4 weeks to get a response back right now.  Is it possible to have such a dramatic recovery as the graph shows?  Yes, if you have a sitewide manual penalty and your penalty gets lifted, AND you have a good base of natural links then some sites can show a dramatic improvement.  But, again, it has nothing to do with getting your disavowed links crawled faster.

I think that tools like Link Detox can have some value in helping site owners (but as I have always said, they don't replace the need for a manual audit.)  But, I have to say that I am concerned about the way that they're marketing this tool.  I think there could be some value, if you have a Penguin hit site, in getting your disavowed links crawled faster.  It's conceivably possible that if you didn't, then Penguin could refresh and your disavowed urls have not been visited and therefore are not disavowed.  But, the way that they've marketed it it sounds like any site that uses this tool can have top rankings again within 3 days of using it and that's quite misleading.

I don't know that anyone knows 100% for sure, but I think it is extremely unlikely that font size would have any bearing on SEO.  The only place where I could see it having an effect is if you were trying to hide something in a miniscule font - this could get you penalized.

I don't believe there is a penalty.  However, It's widely believed that only the first link to each page will count as far as link juice goes.  So, if you have three links on the page that go to the same site make sure that the first one has the anchor text that you desire to rank for.