Yes I've run a couple Merc and Tohatsu both. One was a jet, the other standard prop driven. Both used on 2048, one shawnee the other was a Topwater. Both are about the same hull wise, they are not built for speed!
What I liked about the motor. It was silky smooth running and really quiet. But what I didn't like was that the Merc version was a manual start, and they're tough to yank start being 3 cylinder 4 stroke. The Tohatsu was electric. They seemed to be down on power too, seemed to have plenty of torque down low but lacked up top. I figured I'd see 20mph out of the prop and maybe 16 out of the jet, but the prop was lucky to see 17mph-and that's with only me in the boat (no passenger at the time). About 20 going downriver, 12 going up. Makes for a long trip to the shoals so thankfully it was quiet & smooth. The shifter rod is partially exposed on the one I looked closely at (prop) which I did NOT like at all. Not where I'm fishing at, which is full of moss, weeds, etc. I can't see any rocks getting into it but the moss and weeds sure did. It was a rental and I didn't bother with it much, but the guy at the dock mentioned it when I turned the boat back in. Said every time it comes back from rental, he's got to lift the outboard and clean the junk out of the shift rod area. I cleaned the prop myself (stick it in reverse when it gets "plugged").
I liked them both as far as how smooth they run, but I did not like the weight and the seemingly lack of power. They just felt slow. They were both manual tilt and tilting the prop version was almost impossible from inside the boat, about like the 08-16 Yamaha 25 without tilt assist. It took ALL I had to get it tilted up the one time and I didn't bother with it again afterwards; just kicked it into reverse (which was a little noisy in the gearcase) to clean it off from there on out. And manual starting was not much fun either....seemed worse because the boat did not have a trolling motor so every time I'd float down over a shoal, once I got to a point, I had to turn around, yank my guts out to start it, and then run back upriver. If I had one, it would DEFINITELY be electric start.
Have you looked into the Suzuki or Yamaha yet? Or are they out of the question?
On the boat, I'm not familiar with the Alumacraft but the War Eagle I am...they are built like a tank, handle great, ride great, float level if you leave the plug out, and they are quite comfortable for a jon. The bad? No under deck storage...but it can be added easily if you look at their options. Their website is not great so you're really better off getting a brochure from a dealer which does a better job of describing the features and add-ons, with pictures nonetheless. They are an excellent boat. Again I can't compare it to the Alumacraft because I have VERY little experience with Alumacraft other than their el' cheapo riveted boats (1542, 1230, 1436, etc). Those tend to be a little slower and rougher riding but those are also mass produced with the cheapest fastest labor that they can get.