I would agree with sundialsvc4 that a mechanism where a script writes to a file at startup, and cleans up when it exits, is the way to go. Write the PID to the file. We generally use this mechanism to ensure only one instance of a program is running, but there is nothing to stop you putting multiple PIDs in the file. Either name the PID file according to some convention (e.g. replace "/" in the script path with "-" or some such), or for full generality create a directory tree, on the fly, matching the script path (e.g. a script "/abc/xyz/foo" having PID file "/tmp/pidfiles/abc/xyz/foo.pid").
File locking in this scenario is required, and I don't really understand your concerns about this--after all the script only needs to cooperate with other identical instances of itself, all of which would use the convention of using flock on the PID file. Or put your PIDs in a database.
The only other comment I would make is that you need to handle the case where a script dies before it can remove its PID from the PID file. So check whether a PID is still in use when you start up new instance of a script, and if not, clean up that entry.