I've been lurking on your forum drooling over the new Jeep WK2's and I can't wait to hopefully own one in about a year or so. Although I may not own a Jeep yet, I figured with my past and current retrofit experience, and knowledge, I could answer a few general questions or clarify things a bit more.
First off (I don't want to start this into a flame war), but this is the proper way to equip your vehicle with HID's so I commend the OP for doing this. Reflector housings and even halogen-projectors glare, and in some cases, a lot. I've seen past pictures and threads of people denying this, but it's the truth.
To the OP, great looking retrofit! I was pleasantly pleased to see you used the Gatling Gun 2.0 shrouds which helps to answer the question if the new FX-R 3.0's would fit or not.
To the first time retrofitter and/or someone with little knowledge in this department, I would suggest keeping it simple with the MH1 (Morimoto) projectors unless you have a separate set of lights to work on. Unlike some of the larger projectors 98% of the projector sits inside of the light itself which is then held on by a nut/bolt method. Fairly easy retrofit as generally the only cutting/modification is making the bulb access area slightly larger.
The user who mentioned the FX-R 3.0 losing width is correct. They concentrated on adding more foreground lighting and cleaning up the cutoff giving it the sharpest one I have seen to date. If you're worried about width (which in this case is very minimal) you can always rely on your foglights to do the trick. Previously I had the MH1's equipped in my car, sold them, and purchased the FX-R 3.0's a day or two after they came out. In my opinion, they're the best all-around BiXenon projector out there without spending $600+.
Unlike the MH1 retrofit, the FX-R 3.0s are not held in my a nut/bolt method nor is most of the projector sitting inside of the light (unless you get creative). From what I have seen there are two methods to mounting it; creating your own mounting brackets and/or using a high strength and high heat epoxy such as JB Weld. Size wise it is also substantially larger then the MH1 projectors. The mid-base can take up an entire light opening. On a bright note, I mentioned it was good news the OP use the Gatling Gun 2.0 shrouds as this is compatible with the the 3.0's. In my case the shroud became the most difficult part to integrate into the headlight housing.
Sorry if it looked like a lot of rambling but due to the little time the FX-R 3.0's have been out I figured I would clarify some things about them.
At this point I can't give any advice with cutting or wiring since I don't have the Jeep quite yet. I'd also like to apologize if I look like an idiot doing this.