BouncyCastle undefined length ASN1

I found some bugreports on your problem with possible workarounds outlined. I don't have an appropriate environment to test this myself - sorry. But from the history it looks like it hasn't really been resolved:

1. Bugreport:

This explicitly states problems with BouncyCastle just like you experience. Sebastian Pouliot posts a sample code in comment3 that he thinks can be used (or parts of it) to work around the problem using mono.security.dll. I don't know if your usecase allows to use it. It is shipped with MonoDroid.
He goes into details in this comment and has the example code linked on github: https://github.com/mono/mono/blob/master/mcs/tools/security/makecert.cs

2. There is also someone else who posted a problem with this. BouncyCastle is not explicitly mentioned: http://lists.ximian.com/pipermail/mono-bugs/2010-October/104908.html

His workaround at the end of post:
[Once you have the correct PKCS#12] Quote:

Write the byte[] PKCS#12 into a temporary file and load it with string constructor.

---

Update on source provided in comments

Hope my system worked correctly as it took hours to get it running. But then I got the following working.

The solution is to change the StoreBuilder to UseDEREncoding to true

Small bugfix up front
Finding: You put in a string.empty as password but protected the cert with a password. I think this is not correct. If I put in the password I get the first error again CryptographicException Certificate cannot be coded to valid certificate.

So first I changed this:

certificate = new X509Certificate2(pkcsPath, string.Empty);

to

certificate = new X509Certificate2(pkcsPath, certPassword);

Fix
And now I don't know if this is what you want but after changing it I didn't get an exception but a certificate object.

The complete changes of the "using memory stream" block finally looked like this:

using (MemoryStream pfxData = new MemoryStream())
{
    // **Change 1**: The DER Encoding is enabled on the
    // store builder
    Pkcs12StoreBuilder builder = new Pkcs12StoreBuilder();
    builder.SetUseDerEncoding(true);
    Pkcs12Store pkcsStore = builder.Build();
    // change - end

    X509CertificateEntry[] chain = new X509CertificateEntry[1];
    string certPassword = Guid.NewGuid().ToString();
    chain[0] = new X509CertificateEntry(x509);
    pkcsStore.SetKeyEntry(applicationName, new AsymmetricKeyEntry(subjectKeyPair.Private), chain);
    pkcsStore.Save(pfxData, certPassword.ToCharArray(), random);

    var pkcsPath = pkcsStorePath + "/pkcs.p12";

    File.WriteAllBytes(pkcsPath, pfxData.ToArray());

    // **Change 2**: Use certificate password
    certificate = new X509Certificate2(pkcsPath, certPassword);
    // **Change 3**: Possible to use array instead of filename
    // works as well. Just uncomment
    //certificate = new X509Certificate2(pfxData.ToArray(), certPassword);

}