I have the ultimate answer for you and you will not find this elsewhere online.
I have been through this process and it was a huge pain the a$$
I spoke with John Mueller at Google for years trying to resolve our issues until one day we spoke about hreflang. At which point John said to me that it would be OK to use it. So we played with it and it turned out that we recovered IMMEDIATELY from penguin for a new domain that was hrefland linked from our original site.
So basically this allowed us to keep our original brand name site up while traffic was going to our new co.uk site (in your case .net)
Let say for instance your client is US based. Take the .com site and set it as x-default, then set the new .net site as "en" or if you want to be more specific "en-US".
All Google traffic in english or english from google.com in the US will now start flowing in your non penalised site. the hreflang simply does a swap in those search engines but it happens before the penalty is enforced. So your rankings will return right away depending on where you would now rank after the penalty is lifted and your new content will also be back to their rightful ranking positions. Basically all the suppression is gone.
Dont worry about duplicate content as hreflang handles all that. Its very common for sites to have just a few small changes such as $ to £ or a few spelling changes like color and colour. There is no downside.
If you are clever with the way you code your site you can make it a seamless transition without having to maintain code on two domains. Only took me a few hours to code something up.
The best thing is it opens the door to targeting multiple regions of the world with other languages. (When you are ready).
Hope that answers your question.
Also FYI, when did your manual penalty get revoked? It can take up to a year for your site to be ready for the refresh to consider it OK to lift the suppression. Based on that you may have not been ready for the OCT 2014 refresh and may be waiting for the next one which could be a long way away.