There are a fair number of threads on dieseltruckresource, cumminsforum and turbodieselregister relating to FE. IMO, the ones worth reading have to do with how to drive versus how to mod (adding aftermarket gimmicks). I stay on top of the 3rd Gen trucks, but haven't read as much on 2nd Gen as you have (and looks very clean!!).
mopar1973man has a nice site, and this link to better FE with a CTD is a good start.
Some of the available mpg instrumentation doesn't work well for 3rd Gen so I've not pursued it. But a rule of thumb that seems good is
6&6: 6-psi of boost (intake manifold pressure) and 600-F EGT (exhaust gas temp)
and lower is where best economy will be found.
Were yours mine I'd focus first on record-keeping: average mpg and
average mph as interrelated data to analyze FE. Metro traffic averages 15-mph, and big trucks 50-mph. If your truck is at 22 mph then rolling resistance changes will mean more than aero. If you are above 30-mph then the aero will really start to pay. Not saying don't do it. But take the low-hanging fruit first: LRR tires, MOPAR winter front, year-round use of block heater, no idling, max speed of 58-60 mph, etc.
For aero -- and those boxes -- I'd look to big truck tarp or RV skirting manufacturers for a HD vinyl snap-on bed cover to fit your truck. Add the Dodge Towing Mirrors for yours (no penalty, IMO; or the CIPA towing replacements) to help with backing. Or, a camera on the tailgate. KamperBob has a slick set-up shown in a post here about his rearview camera he "accesses" from the rearview mirror. Ultimately I would rather have a form-fitting fiberglass bed topper with side and rear openings over the boxes extant. I would talk with LEER or ARE about a ladder rack that mounts "flush" in some fashion for when you need it. (Maybe a metal plate across roof plus detachable tie downs?)
Your potential numbers are easily as high as mine. There are 3rd Gen guys with 4WD and auto trans meeting/beating mine. It's all about the calendar year average; or, cents-per-mile.
Here's a
link to a thread where I went on with another big truck driver (that itself includes links) on BSFC versus speed in regards shifting the man trans CTD. Think operating range. The graphs for 2nd Gen (early) I posted recently on the thread here about BSFC numbers (Post 'em!).
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