This is a known issue for this 6th generation civics, actually i had all of those simptoms that you are describing....
On my case i was able to fix it... basically i noticed that there are issues with the rails that guide the windows through the rubber seals, the seals need to be sprayed with graphite, go to a hardware store and get some of that, if you use oil or other kind of lubricants it could damage the seals, the sliicone spray on the brushes is also a good move this will reduce the friction between brushes and the glass window as well as the graphite will do with the glass and the rubbers...
Take your door apart, open it and take a look at the scisor like mechanism, put some grease on those...
and last but not least you will notice that the window has a specific curve, that rail must also have the curb, from time to time and door slams witht he window up that rail tends to straighten up, so you need to find which point of that rail is bent and try to slowly and smoothly move it to its original possition, on my case i used a piece of wood, i found the right spot where the rail would bent and located a specially sized piece of wood there that i glued in, i actually did that about a year ago and it has been working ever since, i even put in new tinted windows and it still works great... Give a shot!!