If money isn't an issue, then just keep the Johnson and fix whatever breaks on it. A 48hp 2-stroke will typically out-perform any 40hp 4-stroke, in terms of speed and hole-shot. Even if it develops internal damage, you'll still spend less money fixing it than you would by replacing it with a new engine. But of course, fixing internal damage will cost you time on the water. So that's a trade-off you have to measure.
But if a new Yamaha/Merc/Suzuki gives you any serious problems, that would be very unusual imo. For the mid-size range, all those brands are reliable if you take care of them.