//1

    Extension basic;
    byte[] enc;
    Asn1BerEncodeBuffer buf = new Asn1BerEncodeBuffer();

    basic = new Extension();
    basic.extnID = new Asn1ObjectIdentifier(ALL_CertificateExtensionsValues.id_ce_basicConstraints);

    basic.critical = new Asn1Boolean(false);
    BasicConstraintsSyntax basicVal = new BasicConstraintsSyntax();

    basicVal.encode(buf);
    enc = buf.getMsgCopy();

    basic.extnValue = new Asn1OctetString(enc);
    request.addExtension(basic);

    //2

    Extension unknown;
    buf = new Asn1BerEncodeBuffer();

    unknown = new Extension();
    unknown.extnID = new Asn1ObjectIdentifier(new int[] {1,2,643,3,123,3,1});

    unknown.critical = new Asn1Boolean(false);
    Asn1UTF8String unknownValue = new Asn1UTF8String("V2QL0020sИванов");

    unknownValue.encode(buf);
    enc = buf.getMsgCopy();

    unknown.extnValue = new Asn1OctetString(enc);
    request.addExtension(unknown);

    //3

    Extension oidExt;
    buf = new Asn1BerEncodeBuffer();

    oidExt = new Extension();
    oidExt.extnID = new Asn1ObjectIdentifier(new int[] {1,2,643,3,123,3,4});

    oidExt.critical = new Asn1Boolean(false);
    Asn1ObjectIdentifier oid = new Asn1ObjectIdentifier(new int[] {1,2,643,3,123,5,4});

    oid.encode(buf);
    enc = buf.getMsgCopy();

    oidExt.extnValue = new Asn1OctetString(enc);
    request.addExtension(oidExt);

// req - полученный запрос GostCertificateRequest 

Asn1BerDecodeBuffer buf1 = new Asn1BerDecodeBuffer(req.getEncoded());
CertificationRequest request = new CertificationRequest();

request.decode(buf1);
CertificationRequest_certificationRequestInfo requestInfo = request.certificationRequestInfo;

Asn1ObjectIdentifier oldId = requestInfo.attributes.elements[0].type; // старый oid
System.out.println(oldId);

Asn1ObjectIdentifier newOid = ALL_PKIX1Explicit88Values.extensionRequest.id;
requestInfo.attributes.elements[0].type = newOid; // новый oid

Asn1BerEncodeBuffer buf2 = new Asn1BerEncodeBuffer();
request.certificationRequestInfo.encode(buf2);

byte[] encodedCert = buf2.getMsgCopy();

// подписываем заново

byte[] signature = GostCertificateRequest.sign(pair.getPrivate(), encodedCert, JCP.GOST_EL_SIGN_NAME, JCP.PROVIDER_NAME);

// сохраняем подпись

GostCertificateRequest.setSign2Request(request, signature, new OID(JCP.GOST_EL_SIGN_OID));

buf2.reset();
request.encode(buf2);

byte[] newValue = buf2.getMsgCopy(); // новый запрос

// Алгоритм JCP.GOST_EL_SIGN_NAME и oid JCP.GOST_EL_SIGN_OID подписи могут менять в зависимости от алгоритма ключа.

Asn1BerDecodeBuffer buffer = new Asn1BerDecodeBuffer(encoded);
SubjectPublicKeyInfo keyInfo = new SubjectPublicKeyInfo();
keyInfo.decode(bufer);
// keyInfo -> subjectPublicKey_.value