I know you are saying "it doesn't feel right" but based on your issues, I doubt it ever will. As long as you avoid the positions and adjustments that are causing pain or discomfort during your average ride, sounds like it is what it is. I tweak here and there but usually only with a change of equipment and after 2 years and many thousands of miles, that has settled down. My last issue on my main bike was about the 6 hour point I was getting numb nuts, eventually got a new seat and it's dimensions are not quite the same so it's been some slight tweaking here and there. I don't think I'd ever be able to track down the impact of changes if I was grossly changing all kinds of things every ride.
I'm not a recumbent owner myself but maybe that would give you a better experience?
Last edited by u235; 02-08-19 at 05:30 PM.