I agree you would likely not have liked a 48RE in your 2003, but that's not a good comparison to a Aisin or 68RFE. I wouldn't enjoy a 48RE, but really liked my '18 Aisin and so far the '22 is doing great and I should be towing soon.
Personally I would look for a HO and give it time, if you don't like it after a while then consider a swap but it will take custom tuning and not be cheap.
I totally agree and I would indeed buy a new one BUT I can't keep myself from saying if I buy a 2500 with the auto and the past issues I will be replacing it at a 100,000 and I can't eat that when it would cost me about the same to swap it to a manual IF I were to stick to the 2018 year which I am fine with. At my age I'll be damn lucky to live longer than another 20 years. LOL Looking on the bright side of it.
Fortunately for myself I have access to some incredible guys that would help me with doing the custom things and for myself it would be piece of mind that if I needed to work on it I could.