Not too bad of a morning, just trying to help keep a standard format of clarity and decent writing. Really no sound reason to make either unnecessarily more difficult than need be. There is a lot of stuff in your signature.
You are asking if you should run your engine stock or modified. I think that is a question for you to answer, not really anybody else. Depends on your objectives.
In my personal opinion, there are not enough people here that have upgraded these parts and documented the results/increases with data (not opinions) to clearly quantify the available gains, yet. Most people don't have access to a dyno, but to even do a timed acceleration run from 0-60mph before and after says a lot over "feels great". Hasn't happened (from me either yet). The 8.3L is run up to about 300hp in near stock MV form before Cummins changes the turbo, injectors, pump, and charge air cooling method, from what we have now. If your target is over 300hp, and you have intentions of changing all the other accompanying fore-mentioned parts, and then you'll be the only one driving it to be sure to monitor EGT's don't go nuclear, then go for the gold from the get go.
The RV owner boards tickle these engines more than done here. A lot can be learned for free there before spending any $ by studying them first. I say do the go-fast parts, and post some performance data results, so we have something to work with as a database. Though you won't have a stock reference for numbers, many of us can chime in with our stock performance numbers as an average to create at least something vs nothing. I have been wanting to do this, maybe this is a good kick-off for it. An MV will never be a race car, but such data will be able to clearly show a performance gain or loss per modification.
So, mod it, and post five timed 0-65MPH runs on the same road/direction.
Like the Brodozers do.