I'm running a Flowmaster Super 40 Series Delta Flow and I really like it. It's not too loud inside the Jeep at all, just loud enough tell it's not a stock muffler. From the outside it sounds nice. You can definately hear it but it's not obnoxious and there's no drone at all. I'm running a DynoMax manderel bent tailpipe (2.25" I believe) and stock manifold & cat.
I had a 50 Series Flowmaster on my previous XJ and didn't really care for it. It had a similar tone compared to my current setup but was louder and droned constantly. Highway drives got old quickly. I was running a stock replacment (crush bent) tailpipe with a straight tip and had a slight leak at the manifold, so I don't know if those factors affected the sound at all.
I listened to about a million YouTube videos of XJ exhausts before settling on my current setup, and IMO the way to go is a Super 40 or 44 Series Flowmaster if you want it loud, or the Super 40 Delta Flow if you want it somewhat quiet. The standard (non "Super", non Delta Flow) Flowmaster 40 and 50 series mufflers just don't sound as good on the 4.0L IMO.
A 2.5" tailpipe will definately be tight with extended shackles. It might work, but you'll probably just have to try it and see. I notice a lot of XJ owners with extended shackles or relocation brackets just cut off the end of the tailpipe before it gets close to the shackle. The DynoMax tailpipe I'm running exits at an angle and I'm pretty sure it might need to be cut off and welded on straight when I install shackle relocation brackets. Kind of a bummer cause it looks nice, unfortunately I think they didn't design it with anything other than stock shackles in mind.