nb heater core i na miata

So I was changing out my heater core in a 1992 miata and I picked up a nb heater core. Now it fits pretty well and the pipes are in an ok position but I have a couple questions. First in the picture it sticks out a little bit so the cover wont fit. Does it really need the cover when you install. Also the hear core doesnt fit exactly becuase of the pipe hole location. Should I modify the heater core box and mabye saw that it fit or what should I do? Or do I really just need an NA heater core?
http://s14.postimg.org/wctfbvush/20141029_201945.jpg

I tried that and decided it was easier to get a NA core. I think I was concerned about the tubes not being supported on the housing.