When I get Kate from the git repository, edit the plugin source, and run Kate, it uses the plugins installed in my system instead of the newly built ones.

You will likely need to setup some environmental variables. First though, you will need to install your freshly compiled Kate to a directory somewhere on your system (where doesn't matter)

Then, you need to create a file in ~/.kde4/env/ called "set-kate-vars.sh"
Place the following into it, replacing $INSTALL_PATH with the location of where you installed Kate.

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export PATH=$INSTALL_PATH/bin:$PATH
export LD_LIBRARY_PATH=$INSTALL_PATH/lib:$LD_LIBRARY_PATH
export KDEDIRS=$INSTALL_PATH:$(kde4-config --prefix):$KDEDIRS
export XDG_DATA_DIRS=$INSTALL_PATH/share:$(kde4-config --prefix)/share:$XDG_DATA_DIRS

Ensure the script is executable (use the Properties dialog, or execute the following command)

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chmod +x ~/.kde4/env/set-kate-vars.sh

If you do not have a ~/.kde4/ folder, but a ~/.kde/ folder instead, simply substitute that in place. They are the same directory, it varies depending on the distribution.

You can ask your system which directory it should be with the following command:

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kde4-config --localprefix

Once the above is done, simply logout and log back in. Attempts to launch Kate should now automatically pick up the new executables, libraries and plugins installed to $INSTALL_PATH.

Note: you can install anything else KDE related to that directory as well, it will also be found without issue.

That kind of works, but there are some problems:

First, I still had to uninstall Kate from my system for it to use the compiled one (which I installed in ~/.local). The other issue is that when I start it the first time, it works (including my modified plugin). But when I launch it again, Kate can't find any plugins (the sidebars and plugin list is empty). I tried installing Kate via the package manager, and that didn't work. When I uninstalled it, it worked again, but also only once!

How do I fix this?

Sounds like the environment variables didn't load. I wouldn't recommend installing in ~/.local as that is used for other things (and may be the cause of this issue)

Also, I noticed two mistakes in my environment variable script, so please replace the version you currently have with the version above. I have edited my post to correct the errors.

It works now.