On the filter...
I think it fits best frame side up, and is wedged between the brackets and the structure of the cowl box at an angle of about 30 degrees off horizontal (forwards up)
I too scraped off the old rubber and when refitting it struggled big time as one side is face up and the other face-down. However, once I had fitted it onto the frame, I dabbed a bit of glue in some key places: corners, swap over points etc. Mine seemed to fit well enough but I figured why risk it coming off.
While there, you may also want to degrease/clean all the mechanisms for the cowl and heater that you find in there. A clean and some new lube made a difference to the workings of my heater levers
The following thread has some pictures that I found useful
http://index.php?topic=5921