I'm seeing a lot of innings where I have multiple runners in scoring position with 0 or 1 out, but end up with 1 paltry run every time. Is there something with the Hit & Run or Base running aggressiveness settings that I could do to put a bit more oomph into my clutch hitting? This seems to be happening to different type teams in different worlds. I'm thinking that I may not be utilizing these settings to my advantage.

There's no such thing as clutch hitting.

Higher H&R seems to decrease homers.    It's definitely a SSS for me as I seldom change that setting.

Baserunning aggressiveness might produce more runs as players will attempt to take the extra base.   However, if your team is slow or you have poor baserunners, you're just going to run into outs.