Hopefully I can help distill this for you and help with advice
Turbos:
I'd skip the stage 1 units and go straight to Pure stg2 DD or HiFlow with 2" snout. Reason on this is they will still spool like stock with appropriate vanos tuning and allow for higher compressor area, same power on 93 with less boost, less wear and tear. There are other options which I like better (Hydra) but Pure is PROVEN and a surefire way to get a reliable set of twins.
Intake:
Since the turbos will be out I'd absolutely get stock location 2" inlets and aluminum outlets installed. This will open up airflow and allow for more of the above. Then since your wife doesn't like turbo noise, get a sealed aFe intake to fit the stock location inlets. I'd also get the ER aluminum charge pipe if not already done, as this both eliminates a plastic pipe which WILL explode on you at an inopportune time (ask me how I know) and deletes the resonator tube which will quiet the cabin a bit, good for wife.
Keep the stock cowl and cabin filters for best quiet.
Exhaust:
Since you have the N55 mids, which I don't recommend (N54/1M mids are superior), you'll want high flow downpipes. I believe AR is the go to for this.
Cooling:
You'll absolutely need an upgraded intercooler. I like the Wagner evo3 comp or the BMS 7.5" Race for this. I've also used the BigTom. Pick your poison. Whatever you choose, go big and get ready to CUT SOME PLASTIC!
Clutch/FW:
I'd recommend against going with a SMFW/Spec clutch if you want something that drives like stock and doesn't make a ton of noise. Read that again for emphasis.
Instead, get an XClutch organic twin disc. AU company. They FINALLY brought it to the US for sale. Supports somewhere around 1000hp, quiet, and stock weight pedal. Stay away from any of the other big twin disc names (spec/motiv/mfactory etc)
Tune:
You can absolutely go with the JB4/MHD backend stack, I did for years and loved it. I'd get your backend custom built for your hardware by Twisted Tuning. OR, go straight MHD custom. N54 tables are continually being unlocked and with MHD WiFi, NLS, Launch Control, Knock tables all coming very soon, I think MHD is going to outclass JB4 in the near future.
Rubber:
Get some sticky tires, you'll need them even with that beautiful ///M rear end.
And before all that we have to mention MAINTENANCE:
Walnut blast, coils, plugs, make sure injectors are functioning properly, depending on mileage and known engine health you may want to go ahead and get a new valve cover with gasket, change out the OFHG and oil pan gasket. IF doing the oil pan gasket, probably a good idea to swap the rod bearings. Since youre doing clutch, its a great time to preemptively replace the rear main seal and guibo. I'd also get new engine mounts and trans mounts. I'd also hugely recommend changing the serp belt and all pulleys/tensioners so the old belt doesn't get sucked into the engine and necessitate a teardown at the worst possible time. There's a ton to do and it all adds up. Sorry for that news.
Have fun!