Replied in the original thread.

There are two (main) types of penalties:

1) manual penalties

In this case, a member of the web-spam team has manually applied a penalty to your site after finding something that was in violation of their guidelines. In order to see if you've been given a manual penalty, simply check the manual penalty section in your Google Webmaster Tools account

In order to remove the penalty, you'll have to file a Google reconsideration request to tell them what you have done to solve the given problem and how you plan to never engage in similar practices again. Google will manually decide whether or not to lift the penalty and sometimes they'll come back to tell you that you haven't done enough (yet) to eliminate the problem that you have been penalized for.

2) algorithmic penalties

These are automatically applied penalties and usually just fixing the problem can lead to the penalty being lifted next time when Google will re-index your site. Sometimes, though, you may also need to file a reconsideration request.

Detecting algorithmic penalties is a bit harder, but if you are experiencing significant traffic drops that happened after your site has been re-indexed or at the same time as automatic search engine penalty updates were introduced, there are great chances that you have received an algorithmic penalty.

You can check for algorithm changes here

https://moz.com/google-algorithm-change

Important: even if you have spotted a significant traffic drop that corresponds to a given search engine update, make sure the drop isn't caused by other technical issues or external factors (robots.txt, server issues, bad redirects, crawling problems, etc)! Also, don't forget that these algorithms usually run over longer periods of time - even several weeks -, so your traffic drop probably won't start on the exact day that the algorithm was reported! However, if you are looking for signs that could indicate a potential penalty, you should pay attention to traffic drops on individual pages or particular keywords, significant number of de-indexed pages or a huge traffic drop overall.

When you are sure that your site has been penalized or excluded from the search engines, you'll have to submit a reconsideration or re-inclusion request.

Requesting a reconsideration or a re-inclusion in the search engines is a painful - and often unsuccessful - process. First of all, you need to understand that search engines receive thousands of reconsideration requests every week and your super-urgent problem is just another file among thousands of other super-urgent cases. So, once you have submitted your request, get ready to wait! Penalty-lifting actions can take weeks or even months and the re-inclusion - if it happens - it's an even longer process. And don't - ever! - try to speed up things! You need to understand that you are not the only one who has urgent issues! Also, you need to be aware that with the search engines, lifting a penalty is not their obligation! Legally speaking they have all the right to penalize or to reject any website. It may sound annoying, but inclusion is a privilege, not a right. This is why making pressures or being impatient will always do more damage than good. Some people will say that you should send them a follow up email to ask how the request is going, but I don't recommend it ...

Hey Patrick,

Those bad backlinks my site suffered from a few years ago now and it took time to recover from. Your first step would be to clean up those low quality backlinks like Marion showed you in here comment here: My Website Is Under Attack! Is Negative SEO Real? I Really Need Some Help. NEVER, EVER accept spam comments. Some members here have said they reword them and keep them but there is a list of IP address that are notorious for spamming, so if THOSE IP address show up in comments you can bet they hurt you to... so delete them too, if you kept them.

While you're at it... you might find a general cleaning of your website (once you've done all the other things that is) is in order to as that can assist your ranking: Cleaning Your WP Database - Does it Really Need to be Done? Hope you find this helpful.

Hi Patrick,

I had this yesterday and posted it on here too. I got it resolved by replacing hyphen with underscore and making sure there was no spaces in the filename. Why am I getting a http error uploading files? Hope this helps.

- Craig

Here are the known culprits:
Bad internet connection (occurs often on wi-fi)
Something other than letters/numbers in file name
File name too long
Those are usually the major culprits. Good luck.