Honestly, I probably make it sound worse than it is. I was actually basically in the same boat as you, though I went through the MS upgrade path instead of starting with all the bells and whistles from the get go. I could have really just left it alone after I did the MS3X upgrade and got it running and never worried about it again, but I wanted to make it act as much like an OEM computer as I could. The car always felt just a little less smooth than the other modern Hemis in the family fleet that I've driven. I was mostly just writing all of this stuff up because I found it interesting and wanted to share everything I had learned over the years. I also basically get 1.5-2 hours of tuning time in every day as I drive to work and back, so it's just been free research time to try out new things and really get things dialed in.
I know at this point I'm chasing that last 5% or something like that in efficiency and general "good running" stuff. My latest commute numbers have got me at ~22-23 mpg door to door round trip, which is probably more like 25 mpg highway and 18-20 mpg in town, depending on traffic. The whole thing just also feels like it runs much smoother. The main "issues" I've had have just been my AFR numbers floating around as the ambient conditions change. The car still runs fine and if I didn't have the gauge to look at I'd probably never know any better. Mostly just trying to really dial it in for fun now.
I also started with literally zero tune in my car. I bought the MS2 used, so I didn't have any kind of base tune to start with and had to learn from scratch.