@cylestene
to me you seem to be the foremost authority on pakwheels when it comes to 8th gen civics so i have a few questions for you later in my
Thank you for that respect 
After hearing your story, I'm quite shocked. My Civic has been with me for the last 3.5 years now and has been largely trouble free. To me it looks like you were sold a lemon and that can be troublesome especially in a car which has become 10x more complicated than its predecessor (and its a first for Honda as the fit and finish of this car is far better than the previous generations, it feels more upscale than its counterparts).
Allow me to answer your questions and I understand that I'm answering them late but I just read your post a while back:
(1)the cars been driven 3000km so yesterday i decided to clean all my cars filters and check fluids. again i was disappointed to learn that when i opened the glove box and took out the CABIN air-filter tray...it was EMPTY!!! i paid 1.75million for a car and they didn't put a freakin cabin filter! is that the norm for all 8th gen civics or for 2009 models or was it just my car?
Atlas is not giving cabin filters for some reason; its part of their cost cutting I suppose and is definitely NOT justified for a car which costs this much. I put one in myself when I got the car. You can get them from any Honda dealership in USA, I don't think its sold locally.
(2) what happened to the boot lid insulation (lining)? all the rear lights' wires and number plate nuts and bolts are visible. i suspect this might be contributing to the rattling sound.
also the plastic enclosures for the pivots/hinges of the boot lid are missing.
both these items are present in the previous honda city!
Yet again cost cutting, the hood and boot insulation are totally non-existant in the local model.
(3) i too suffer from a "stiff" 2nd gear even though i drive and change gears very gently and shift at around 2250rpms.
What exactly do you mean by "stiff" gear? Do you mean its hard to shift into, or out of? The car does have one issue which I believe is drive-by-wire related and thats the slight rev-hang it has around the peak 2nd gear rpm levels. But its barely noticeable, is that what you're referring to?
After all these years here are the issues I faced with my car:
Sticky driver side window; railing replaced as per TSB in warranty but the issue pops back. The railings are defective to date in all models internationally. Its the design of the railing/track which causes this. It is very much a problem in areas which suffer from dust (especially karachi). WD-40 is the best solution.
Engine mount (front right) wears out fast. This is the oil filled kind apparently and is delicate. Apparently the khaddas and potholes of Pakistan are too much for it.
My car's knock sensor went bad and was replaced for 2,500 RS (this was in 2008).
Aside from this the car has been largely trouble free. Especially considering how much I have tinkered around with my car; its been very reliable. To this date it is squeak, squeal, hiss, and clatter free as far as the cabin noise goes. No joints have started squeaking yet.