...my shadows come out as a bunch of dots rather than a soft shadow. How do I remedy this problem?

raise render quality settings.

Is there a specific area? I'm already using a user rendering setup to optimize my time. Is this an AA issue?

Not really, it depends more on the number of rays, in other words, it's a resolution issue, you need to raise the resolution of rays to make a whole of what now appears to be a discrete series of blobs. Sometimes not even Ultra is enough, you may have to take note of the Ultra settings and then go into User custom and use even higher values. An alternative is to use image maps instead of raytracing the shadows.

I don't know what your exact imaging requirements are but as Orio said, Shadow Maps are a really good alternative to getting rid of Ray Traced noise, etc. They go up to 4096x4096, but are adjustable, and can even be used with other Ray Trace lights...

An alternative is to use shadows maps instead of raytracing the shadows, for me the best solution... in my image i use always shadow maps, also GI helps...