Keep the resonator if you want to maintain that little bit of torque around 4k.
I'm currently working on a JR looking intake. I'm using the stock resonator and plumbing but it wil be shortened a good bit, hacking up the air box a bit (and flipping it over so the open end is facing semi-upward) and positioning it (with support arms for the box/AFM). The only issue I see is extending the AFM wiring. I was told a while back that you can slice the harness a bit and get some extra slack, but I'm going to need another foot or so, lol. Oh well, soldering gun here I come.
I'll post pics one day when I finish it....whenever that is. However, if all goes well, this will look very OEM and clean...not a hack job or whatever.