Reddit reviews Computational Electromagnetics for RF and Microwave Engineering
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Used Book in Good Condition
Since you're wanting to work with the step-response, you are probably looking at a FDTD (finite-difference time-domain) solution. One open source implementation of this is OpenEMS. It's a simple enough concept that if you have some time, you could write your own implementation: it's basically just solving Maxwell's equations repeatedly at a number of points through your domain.
Most software will let you work in 3 dimensions, the limit will simply be on the computing speed/power you have access to. Any program will let you program different media, and study their effects. Finally, many programs will not calculate the step response directly, but will calculate in the frequency domain, which you can convert to step-response using a Fourier transform.
ANSYS HFSS is a good commercial software for this purpose, and is about on-par with the difficulty of any other program out there. These software programs are complex because they have to be a CAD program (for you to design the shapes and structures), and then a simulation program, which has a lot of complexities on its own. Other software out there is FEKO (3D, good for antennas), ADS (2.5D, mostly for circuit board design), and NEC (free, and best for antennas made of thin wires).
Computational electromagnetics is a huge subject, and there is a right tool for every application. The problems you're trying to solve don't sound too complex, but you still need to know what you're doing in order to get accurate results from the software. Some good books on the subject are this, which gives an introduction to the techniques used by many of the programs, and this, which gives you information on how to build your own FDTD solver using Matlab.
Best of luck with your simulations.
Wanted to chime in besides Balanis (he explains MoM in antenna theory as well but much better in Advanced Emag) you could try this this video course
or this book which I learned from myself
Also if you like using python you could pick up an intro to computational physics book with python and then look up FENICS, MEEP or gprMax