how's your tolerance to resonance? some guys can tow 15,000lbs with 5" straight pipe and not have any problems.
I'm sensitive to it. I would hate to recomend a 5" exhaust system to you and it be unbearable while towing... even with a muffler! The bottom line is 4" or 5", you should be out from under the exhaust system for about $500
the first setup I had on my '06 was a cheap 5" system with a 51" Donaldson M090535 muffler. I had less than $400 in it including shipping. very low resonance, but still had a little. adding a 5" resonator probably would have nixed the rest of it.
I'm not running 4" off the turbo (aftermarket turbo) back to about the axle, and then 5" tailpipe. straight pipe.
But I also have over 3 rolls of Raam Audio sound deadener on the floor and back wall of the truck. There is a bit of a resonance point still, but I don't tow and I drive above or below that point. I've got a Corsa muffler that I'm planning on installing maybe one of these days
I am a Smarty koolaid drinker... They've got great tunes, lower exhaust temps, you can tweak characteristics of the tunes, and you can download different tunes, etc. You don't need the full Smarty, but the Smarty Jr. is limited and if you ever do any transmission work, you'll have outgrown the Jr. I think retail on the Smarty is $685, but you can get them cheaper.
the highest recomended setting for the stock auto is level 3 which is about a 70hp tune. I ran my truck on 5 which is 90 and the tranny looked great when we tore it apart, you just have to be smart about the power. If your'e going to be towing, I would set it on level 3.
You don't need gauges at that power level IMO
on the intake side? really a good drop-in filter will be sufficient... and actually, converting over to a 6.7 air box and using one of their drop-in filters will probably outperform most aftermarket setups! but, if you're one of those guys that really likes to hear the turbo scream, a full aftermarket setup with the tube, heat shield, filter, etc. will give you that great sound and good performance.
You can piece together your own filter/pipe setup, but with your proposed budget, you've got plenty of room left for an intake setup.