Hi, Ann-

There are indeed multiple instances of python:
+ the ones with "miniconda3" in the path are from your conda setup
+ the /System/Library/* one is from the basic Mac OS setup
+ the /opt/sw/* one is probably from macports, judging by path (I think that installs under /opt/; fink installs under /sw by default)
... but that might not be such a problem.

You can type "which python" in the command line to see excactly which python your current shell is using. The afni_system_check.py shows you that as well:
+ for current bash, it is: /Users/achoe2/miniconda3/bin/python
+ for earlier bash, it is: /Users/achoe2/miniconda3/envs/py27_afni_tiny/bin/python
I think that means that at present, your default conda environment python is just the "base" one (a Python 3.8 that liekly does not have any other modules loaded), whereas before it was one you created (a python 2.7, likely with a couple things listed for AFNI installation, judging by the name).

If you type "conda env list" in the terminal, it will show you all the environments you have to choose among; the one that is currently "active" has an asterisk just after its name. What is the output if you have "conda env list"?

To have a particular conda environment active by default in your shell, you can put "conda activate [name]" after the conda initialize block of code in the shell's "~/.bashrc" or "~/.cshrc" file. For example, you could put "conda activate py27_afni_tiny", or something with Python 3.* that has additional modules.

Another question: from your setup, it looks like you have tcsh as your default login shell, but you switch to using bash... would you prefer to have bash be your default login shell?

--pt

ps: for clarification, the "whee" was not to suggest that this was easy, but actually meant ironically that setting up conda with tcsh is so complicated...