you on about your top engine cover?
yep, should have probably stated that.
you got any pics of your engine cover? and possibly a bigger pic of the bay?
ill get some, only one i have atm is this one, don't think it well be much help.

but you can see the two pipes at the top, one with yellow tape and one with red and just in view is the pipe at the front for the AC just popping up above the blue screwdriver.
can you not just trim the area where its rubbig? or fit some fabric tape to stop the chafing. sounds liek the cover isnt fitted right if its rubbing on stuff though. can you bend the a/c pipe retaining bracket a bit to move it out the way?
I am hoping that's a last resort cutting the cover. the cover screws down fine i think it may just be the engine vibrating to much, can you tune the engine? or can the engine go out of sink or anything like that?