The seat height is something that you really do not fool with once you get it dialed in. The height you select is about the bend in your legs at the knee joint at the bottom of the pedal stroke. I have found that even very minor changes make my pedal stroke feel not "right". How your rear feels should have nothing to do it it.

Your fore and aft alignment of the saddle has to do with how you are lined up over the pedals. I forget the exact way of doing it because I do it by feel now.

I tend to nose up the saddle very slightly but keeping it level would probably work also.

The thing is that different saddles can give you markedly different feelings in your bottom. At the base of your pelvis are two bony nobs, the ischeal processes. There is one on each side. The idea is that the ischeal processes should make firm contact with the saddle. If the saddle is too narrow, the saddle will be between the ischeal processes and your weight will be suspended on soft tissues which is not a good thing. If the saddle is too wide, you get a different uncomfortable problem. Near where I live, there is a bike shop that has a "butt-o-meter" for lack of a better term. You sit on it. Your ischeal processes form a little image and they can then suggest saddle which will fit correctly. Otherwise finding a saddle can be a bit hit or miss. I have heard of some DIY methods of making the same measurement but I don't remember the specifics.

Be that as it may, even with a properly fitting saddle, it will take some time in the saddle before things "toughen up". You can expect some initial soreness after rides. But largely go away.