Hi Marc,
You've written out a very detailed question, and I think you are in the right direction with the disavow. You already stated how you have spent a significant amount of time on your link cleanup procedure, and have documented a lot of the work you have done and the outreach you've done to try and clean up your backlink profile created by your previous SEO. I would submit this to Google in your reconsideration request after doing the disavow - it can't hurt to submit the reconsideration request. But keep in mind, if you got hit by an algo penalty like Penguin and not manual action, the webspam team won't be able to remove the penalty. Only if the webspam team applied a manual penalty to your site or part of it will the reconsideration request help.
In terms of the disavow, as shared by the webspam team (Matt Cutts, Joh Mueller), take a machete to your problematic backlinks - http://www.seroundtable.com/google-disavow-machete-16844.html. If you find domains that have problematic links on them, instead of trying to disavow each page with probleatic links, use the domain: operator and disavow the whole domain/subdomain. Don't be precise and surgical, but use a machete on those problematic domains and links. Once this has happened, I'd see what happens with the rankings.
In terms of Google carrying over the penalty to your new .com domain due to brand association, I wouldn't worry about this. If you were in fact hit by an algorithmic penalty based on links, if the links remain pointing to the old domain, and you don't give the search engines indications that they should replace the old domain with the new one (301 redirects, change of URL via webmaster tools), there should be no reason the engines would pass over the links and the penalty to the new domain. I don't believe the algorithmic link penalty is based on your brand, but rather on the specific site and that site's backlink profile. So if you do start from scratch and don't 301 redirect to the new domain, you are in effect starting from scratch. You many not rank in the beginning, but that's not because the link penalty transferred over, but your site may not have enough link equity on its own to rank.
Either way, good luck with whichever path you choose - I personally hope the disavow helps you and you can salvage your current site, so you don't have to put all of the hard work and effort you put into your old site in the trash.
Good luck,
Mark