Ok,
There is probably an easier way but the following may work.
1. Attach a menu item to a script which sets and exports an environment variable (i.e. var='run_custom_script)
2. The script then starts a shell which should now contain the set variable.
3. You user startup scripts (.profile/.cshrc/.kshrc etc) can look for this variable and if found then run your scripts you need running.
4. Once the scripts finish the shell should still be there for anything else you want to do with it.
5. On exiting the shell, control goes back to the underlying script which can then unset the variable and exit.
As I said, there is probably a simpler way but the above should work with minor tweeking.
RB