Subscribed to this thread and looking forward to seeing your truck back to 100%. I bought my wife a 2001.5 Ram 2500 in Patriot Blue with 2 tone silver off of Craigs list from an owner who had ALL the services done at the dealer where he bought it. Eventually I will restore both trucks much in the same fashion you have. REALLY sorry about your baby being stolen. We as a nation need to go back to prison restitution/work camps for crimes like this.
Just my humble suggestion........get rid of that gauze/oil air filter. These types of filters are absolutely NOT suitable for diesel engines and will eventually ruin them by letting very fine dust particles get by the filter and into the engine wreaking havoc with pistons, piston rings, turbos, oil, etc. Use a good quality paper filter. A Donaldson B105006 or a Feetguard AH19037 BHAF with a nice matching blue Outerwares prefilter over the BHAF is a tough combination to beat for excellent air flow and particle filtration.
Best of luck with your restoration. I will indeed be looking forward to your future posts.