Thank you for the replies! The `guix refresh --list-transitive` command was helpful for what I was trying to do, although I now think I was going down the wrong path.
While checking things in my system, I noticed that the guix command that was invoked under a root shell pointed to a different binary than under my user's shell. I assumed that having different versions of guix simultaneously operating on the same store could cause lots of problems which are difficult to explain, so I decided to reinstall the system from scratch, which did not seem too troublesome since guix's commitment to declarative configuration makes re-installation very easy. I had some issues where I saw error messages similar to https://issues.guix.gnu.org/56005, which was speculated to be due to difficulties communicating with the server. So I just waited a few days each time this happened and re-tried, and eventually I got the bare-bones config from the installer ISO to install to my machine. However, I am still seeing a similar problem to before, when I try to `guix home reconfigure` the process starts building git-minimal. I stopped it immediately instead of waiting to see how far it got because this seemed to be the same behavior. I also found that `guix repl` produces an error that the __libc_pthread_init symbol is undefined in libpthread.so, although readelf tells me that the symbol exists. The symbol value is null which seems weird but I don't spend a lot of time looking at readelf output and every symbol in the '.rela.plt' section has a null value, so maybe this is expected. The error occurs if I run guile without any arguments, from the guile-wrapper used by guix. Running the system guile command works fine. Also, the error only occurs in the guix from `~/.config/guix/current/bin/guix`. This runs by default because it is in my path first, but if I run `/run/current-system/profile/bin/guix repl` then the program executes without issue. I'm not sure if the one in /run is an older version that I shouldn't use or if it's the one that I should be getting when I run plain guix (without a path). IIUC, `guix pull` is supposed to update the files in `~/.config/guix/current` to be the correct ones, and the guile-wrapper is pointing to an absolute path of libpthread in the store as it should, so I'm not sure how this error is occurring. The system has not changed much from the bare-bones config, I just added tmux, vim, and nss-certs to make the TTY easier to use and make sure I could download https urls. This seems strange. I'm going to keep looking into this, but hoping that something above might sound familiar to someone.
