Welcome. I'm not to familiar with HP tuners (I've only used EFILive), but the tuner that created your files might have some more insight if that's the platform he uses. Otherwise, a nice scanner might do the trick. I do wonder if you don't have a tuning issue if you're still getting the pop up's...
Diesels in general aren't "money hogs". The only extra maintenance in general is around the fuel filter (most guys change those every 15-25K).
Newer modern diesels do have emissions issues to overcome sometimes. Sometimes you find a good healthy truck, and sometimes you do not.
Welcome to...
Welcome!
I'd recommend reading through some threads here:
https://www.ecodieselram.com/forum/forums/ecodiesel-performance.28/
Plenty of reviews and opinions on the tuning matter. :)
Welcome! You're gonna get mixed reviews on that for sure, I'd recommend this section and look at a few threads:
https://www.ecodieselram.com/forum/forums/ecodiesel-settlement-information.36/
I think most people actually drive like that deleted. I myself had a truck that was missing some parts and I did enjoy the extra power. The youngin's out there that buy one and make youtube videos blowing smoke everywhere ruin it for everyone!
Just like politics and religion, we all have our beliefs. Let's not let delete vs non-deletes be a new addition to that category.. it's almost like my oil is better than yours... :D