The problem is I would be guessing at the clearance needed for the parts. Without having a PC-04 kit in hand to make some measurements.
How much clearance is there beneath the shoulder pieces? and how far back are they set from the smokestacks/exhaust pipes?
I could certainly try based on guesswork, but the question is would you be willing to try it out when I was done?
As far as filing it down to get clearance, certainly. But I cant say how that would affect strength. And depending on how much you had to remove, it might affect the ability of the cannons to combine into one weapon.