I can't really help you on the refitting of the trim, but I have a brand new OEM rubber trim for an ek/ej (ek9 may be different), that I can sell you for half the price.
I know this is a bit of a thread revival but for future reference - the windscreen trim cannot be replaced without taking the windscreen out on a EK9 or other EK Civics. The reason is that the glass sits in the molding and the molding itself is bonded to the car. When I removed my windscreen it was really difficult to get the glass out of the molding and the chances are you'd break the windscreen doing so. In the end I got a new Pilkington windscreen and molding from local windscreen fitters (£132 for both inc VAT).