I recognize this situation is difficult and a lot of emotions are involved. I would like to be helpful which is why I have volunteered time sharing the results of my experiences...to help others such as yourself.
I sympathize with your situation. A manual penalty for manipulative links has driven some companies out of business, other companies have been forced to lay employees off, and many SEO companies lost clients. I fully understand the impact.
Please keep in mind the original Q&A was asked and answered. You added to this thread stating "This is exactly what happened to us. We have removed over 600K links so far but still not enough for google. We are out of luck now because we cannot get any more links removed! ".
If you are requesting assistance I'll do whatever I can to help, but it is upon YOU to let us know your situation and how we can help. You stated you removed 600k links. And? For my first client I removed 3.5 million links and the penalty was not lifted. It makes no difference how many links you remove per se.
You also shared you are "out of luck" because you could not remove more links. Google has repeatedly lifted penalties for sites who were not able to remove all the links. Why is this statement relevant?
I humbly suggest the problem is neither Google nor me. You have a problem with how Google is ranking your site. We can hopefully agree on that statement. Based on your replies, the information you are sharing is not relevant to removing the penalty. You can say "I removed 600k links! How is that not relevant" My first client removed 3.5 million links and the penalty remained. Google does not care how many links you remove. The penalty is in place because of the links which remain.
Next, you mentioned the remaining links are impossible to remove. Here is the information which is helpful to Google:
1. Did you send a polite e-mail requesting link removal to the domain owner?
2. Did the e-mail contain a list of all links from that domain to your site?
3. Did you send the e-mail to the e-mail address on file with the WHOIS registry?
4. Did you also send the e-mail to any e-mail address on the site (if different)?
5. Did you also use the site's Contact Form (if available)?
6. Did you save a copy of all communications sent along with the date they were sent? Are you making these communications available to Google?
7. Did you verify which links were removed? Did you follow up with webmasters request regarding link removal?
IF you began with a comprehensive list of all known links to your site (i.e. not just Google WMT links and not just Google + OSE links but a comprehensive list from many sources) and IF you properly identified all the manipulative links and then followed the above process, Google will remove the manual penalty. The only other requirement is you admit any wrongdoings and commit to honestly following Google's Guidelines going forward.
I hope you find this information helpful. If not, I will simply accept you may be beyond my ability to assist.
Good Luck.