Somewhat vague answers...but to summarize the important points:
* The disavow tool is applicable to Penguin hit sites, but doing a reconsideration won't help in this case
* You should attempt to remove links and not just to diavow links because apparently google can look at your history:
"In particular, Google can look at the snapshot of links we saw when we took manual action. If we don’t see any links actually taken down off the web, then we can see that sites have been disavowing without trying to get the links taken down."
* Google canonicalizes url variations well, but for pages with index or trailing slash variations, you might want to include all to be safe
* Several week delay to several months (note he didn't say if this was for Penguin)...this was horribly vague
* Lop off the www variant to get the www.domain.com/badlinks.html and domain.com/badlink.html
* Disavowed site data won't be used that much for spam data. "We may do spot checks, but we’re not planning anything more broadly with this data right now."
When Cutts was asked how long it might take to see any effects from submitting a disavow list, he said:
It can definitely take some time, and potentially months. There’s a time delay for data to be baked into the index. Then there can also be the time delay after that for data to be refreshed in various algorithms.
"refreshed in various algorithms" seems to refer to alogrithmic penalties, not to manual penalties. It could mean that submitting a disavow list for a Penguin-hit site definitely could have positive effects, but they wouldn't show up in the SERPs until the next Penguin update or refresh.