Как добавить сертификат в магазин?

Лучше создавать сертификат с помощью специальных инструментов, таких как makecert. , openssl и т. д. Затем, согласно Сериализация сертификатов вы можете добавить его в сертификат store.
Изменить:

makecert.exe -$ individual -n "CN=Test Signing Cert" -r C:\Users\public_v2.crt

потом

#pragma comment(lib, "crypt32.lib")

#include <stdio.h>
#include <windows.h>
#include <Wincrypt.h>
#define MY_ENCODING_TYPE  (PKCS_7_ASN_ENCODING | X509_ASN_ENCODING)
void MyHandleError(const char* s);

int main()
{
    // usage: CertExtract certpath

    char keyFile[] = "C:\\Users\\public_v2.crt";
    BYTE lp[65536];

    SECURITY_ATTRIBUTES sa;
    HANDLE hKeyFile;
    DWORD bytes;

    HCERTSTORE         hFileStore;

    PCCERT_CONTEXT  certContext;
    HCERTSTORE         hSystemStore;

    sa.nLength = sizeof(sa);
    sa.lpSecurityDescriptor = NULL;
    sa.bInheritHandle = FALSE;

    hKeyFile = CreateFile(keyFile, GENERIC_READ, FILE_SHARE_READ, &sa, OPEN_EXISTING, FILE_ATTRIBUTE_NORMAL, NULL);

    if (hKeyFile) {

        if (ReadFile(hKeyFile, lp, GetFileSize(hKeyFile, NULL), &bytes, NULL) && bytes > 0) {

            certContext = CertCreateCertificateContext(X509_ASN_ENCODING, lp, bytes);

            if (certContext) {

                printf("yay!");

                /*if (hFileStore = CertOpenStore(
                    CERT_STORE_PROV_FILENAME,
                    MY_ENCODING_TYPE,
                    NULL,
                    0,
                    L"testStor.sto"))
                {
                    printf("The file store is open. Continue.\n");
                }
                else
                {
                    MyHandleError("The file store did not open.");
                }*/

                if (hSystemStore = CertOpenSystemStore(
                    0,
                    "CA"))
                {
                    printf("The CA system store is open. Continue.\n");
                }
                else
                {
                    MyHandleError("The first system store did not open.");
                }

                if (CertAddEncodedCertificateToStore(
                    hSystemStore,
                    MY_ENCODING_TYPE,
                    certContext->pbCertEncoded,
                    certContext->cbCertEncoded,
                    CERT_STORE_ADD_NEW,
                    &certContext))
                {
                    printf("Another certificate is added to the file store.\n");
                }
                else
                {
                    MyHandleError("The new certificate was not added to the "
                        "file store.");
                }

                /*if (CertSaveStore(
                hFileStore,
                MY_ENCODING_TYPE,
                CERT_STORE_SAVE_AS_PKCS7,
                CERT_STORE_SAVE_TO_FILENAME,
                (void*)L"testStor.sto",
                0))
                {
                    printf("Another certificate is saved to the file store.\n");
                }
                else
                {
                    MyHandleError("The new certificate was not added to the "
                    "file store.");
                }*/
                //-------------------------------------------------------------------
                // Free memory.

                CertCloseStore(hSystemStore, 0);
                //CertCloseStore(hFileStore, 0);
                printf("The program ran without error to the end.\n");

                CertFreeCertificateContext(certContext);
            }
            else {
                printf("Could not convert certificate to internal form\n");
            }
        }
        else {
            printf("Failed to read key file: %s\n", keyFile);
        }
    }
    else {
        printf("Failed to open key file: %s\n", keyFile);
    }

    CloseHandle(hKeyFile);


    return 0;
}

//-------------------------------------------------------------------
//  This example uses the function MyHandleError, a simple error
//  handling function, to print an error message to the standard  
//  error (stderr) file and exit the program. 
//  For most applications, replace this function with one 
//  that does more extensive error reporting.

void MyHandleError(const char* s)
{
    fprintf(stderr, "An error occurred in running the program. \n");
    fprintf(stderr, "%s\n", s);
    fprintf(stderr, "Error number %x.\n", GetLastError());
    fprintf(stderr, "Program terminating. \n");
    exit(1);
} // End of MyHandleError