So here's the hoops I'm jumped through:
Installed new root certificates.
Added the two adresses in trusted zones in IE.
Installed the certificate.
Disabled my firewall.
Made sure system dates wore correct (in windows and BIOS).
Changes regional settings to english (US).
Restarted NL about 50 times.

Tried the alternate port settings in NL.
Cleared the IE cache (I even tried clearing everything so now I have to put in all my passwords all over again).
Tried setting IE security to Low.
Tried the alpha version (3.9b9T1) of NL.
Checked the HOST file.
I also tried a bunch of random stuff that I don't even remember now.
Status:
Instead of just hanging at awaiting response it now spits out an error message after quite some time (Unable to recieve a reply from the ...").
Also, in the 3.8b8 release which is dependent on IE I could see the newspage. In the 3.9b9T1 release I can't see the news page.
So I've spent all this time, put my computer at risk, lost my passwords (due to overdiligence on my behalf but still) and still I can't get the damned thing to work.
Important to note is that on my side NOTHING has changed from the day SS worked 'til the day it stopped working.
When the problems started I could sporadically reach the XXX search and one single time I could reach the general SS search.
Now I can reach neither.