Slowly modding my 2009 mtb bike (help make it comfier)

When I first started traveling, instead of buying a different bike, I decided to use the one I already had, even though it wasn't the "correct" one. It's a 2009 Rockrider 5.2 that was gifted to me when I was younger by an already deceased relative, so I'm very fond of it.

Slowly, I’ve made some changes to it: on my first trip (200 km), I got a more comfortable seat and a pannier rack. I didn’t have panniers back then, so I just zip-tied some random bags to it. I also used an MTB tire in the front and a used touring tire in the back.

I just came back from my last trip, now with two proper 20L panniers (way better than the random bags, who would've thought?), proper touring tires, foam grips, handlebar horns, and an adjustable stem (which I now always keep at a 40º angle). I've also sewn a custom bag for the frame and a stem bag (inspired by myog)

I find the original riding position of my bike too aggressive for touring, and I’d like to make it more upright, hence the adjustable, higher stem. Do you have any recommendations on the best way to achieve this? Is it better to use an angled stem like mine, stem extenders, or a different handlebar?

I need to take some time to try and do a bike fit too, i feel like the seat should be further back: as it is, i tend to push the pedals with the center of my foot. If you have any tips on things I could change about it that would make it a better bike to travel, feel free to chip in!