Make sure that you are using the Pardiso matrix solver (default in PrePoMax, but it’s important to ensure this). CalculiX may not be able to hanle such large numbers of modes, but you could perform a separate run with higher lower bound to start from e.g. half of that range.
Also, to make sure PrePoMax won’t interrupt such a large run, try submitting it from the command line as described here: Using standalone CalculiX
Unfortunately, there’s no way to limit the modes to the ones with a specific response apart from modifying the supports (which would of course also shift the frequencies).