Здравствуйте. Xmlsec, xalan, serializer есть в зависимостях? В lib/ext? Jcp использует Xmlsec 1.5.0, см. в папке dependencies дистрибутива jcp.

private static final String SMEV_URL = "http://smev3-d.test.gosuslugi.ru:5000/ws/smev-message-exchange-service-1.3.wsdl";

String contentString = xmlMapper.writeValueAsString(rootAssessmentBody);

initFileStore();

DigitalSignatureFactory.init(CRYPTO_PROVIDER);

KeyStoreWrapper keyStore = DigitalSignatureFactory.getKeyStoreWrapper();

PrivateKey spPrivateKey = keyStore.getPrivateKey(PERSONAL_CONTAINER_ALIAS, PERSONAL_CONTAINER_PASSWORD.toCharArray());
X509Certificate spCertificate = keyStore.getX509Certificate(PERSONAL_CONTAINER_ALIAS);

PrivateKey ovPrivateKey = keyStore.getPrivateKey(CONTAINER_ALIAS, CONTAINER_PASSWORD.toCharArray());
X509Certificate ovCertificate = keyStore.getX509Certificate(CONTAINER_ALIAS);

MessageExchangeEndpoint messageExchange = MessageExchangeEndpoint.create(
SMEV_URL, FTP_ADDRESS, ovPrivateKey, ovCertificate
);

String messageID = messageExchange.generateMessageID();

DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
Document document = builder.parse(new InputSource(new StringReader(contentString)));

Element content = document.getDocumentElement();

// подготовка вложений
List<InAttachment> attachmentList = new ArrayList<>();
// TODO тут формируем список вложений, если они есть

// можно включить трассировку запросов и ответов (по умолчанию выключена)
InterceptorStorage.getRequest().setIntercept(true);
InterceptorStorage.getResponse().setIntercept(true);

try {
// используем ЭП-СП:
PersonalSigner signPersonal = new KeyPersonalSignerImpl(spPrivateKey, spCertificate);
messageExchange.sendRequest(messageID, content, signPersonal, null, attachmentList);
} catch (Exception exception) {
// тут могут быть разные exception в зависимости от ответа сервиса
exception.printStackTrace(System.err);
}

// через InterceptorStorage можно получить конверты запроса и ответа
System.out.println(InterceptorStorage.getRequest().getString());
System.out.println(InterceptorStorage.getResponse().getString());

}

ru.voskhod.crypto.exceptions.SignatureProcessingException: org.apache.xml.security.signature.ReferenceNotInitializedException: No message with ID "Can not perform transformation urn://smev-gov-ru/xmldsig/transform" found in resource bundle "org/apache/xml/security/resource/xmlsecurity"
Original Exception was org.apache.xml.security.signature.ReferenceNotInitializedException: No message with ID "Can not perform transformation urn://smev-gov-ru/xmldsig/transform" found in resource bundle "org/apache/xml/security/resource/xmlsecurity"
Original Exception was org.apache.xml.security.signature.XMLSignatureException: No message with ID "Can not perform transformation urn://smev-gov-ru/xmldsig/transform" found in resource bundle "org/apache/xml/security/resource/xmlsecurity"
Original Exception was org.apache.xml.security.transforms.TransformationException: No message with ID "Can not perform transformation urn://smev-gov-ru/xmldsig/transform" found in resource bundle "org/apache/xml/security/resource/xmlsecurity"
Original Exception was javax.xml.stream.XMLStreamException: Non-default namespace can not map to empty URI (as per Namespace 1.0 # 2) in XML 1.0 documents