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I am not quite sure, if it is a good idea, but I personally would insert log entries, that tell you at what point your application crashed and insert a single, but large try-multi catch block at the end of you class. For example:

 try {
 keyStore = KeyStore.getInstance("JCEKS");
 } catch (KeyStoreException ex) {
 throw new CryptoException("Error saveKey | KeyStore.getInstance", ex);
 }
 try {
 keyStore.load(null, null);
 } catch (IOException | NoSuchAlgorithmException | CertificateException ex) {
 throw new CryptoException("Error saveKey | keyStore.load", ex);
 }
 try {
 keyStore.setKeyEntry(userName, key, password.toCharArray(), null);
 } catch (KeyStoreException ex) {
 throw new CryptoException("Error saveKey | keyStore.setKeyEntry", ex);
 }
 try {
 keyStore.store(new FileOutputStream(userName + ".jceks"), password.toCharArray());
 } catch (KeyStoreException | IOException | NoSuchAlgorithmException | CertificateException ex) {
 throw new CryptoException("Error saveKey | keyStore.store", ex);
 }

would convert to

try {
 log.info ("Get an instance of the keyStore");
 keyStore = KeyStore.getInstance("JCEKS");
 log.info ("load (null,null)");
 keyStore.load(null, null);
 log.infor ("Set the key entry for the user");
 keyStore.setKeyEntry(userName, key, password.toCharArray(), null);
 log.info("store in the keystore");
 keyStore.store(new FileOutputStream(userName + ".jceks"), password.toCharArray());
} catch (Exception e) {
 throw new CryptoException ("Execution failed! See logfile for more info", e);
}

I think this is far better readable.