I'm having problems inserting a new CA certificate with privatekey in the Root certificate store of the localmachine. It you do need save private key on Machine key store, that you should at least protect the key for reading only for some selected users and not from Everyone. Then you can export certificate with or without private key with respect of Certificate Snap-In (for mmc.exe). You should import it in Root or AuthRoot in localMachine on every (or many) computer of your organization, but you should import the certificate without the private key.
You should import CA certificate with private key on the computer on one computer and only for the user who will issue other certificates (who will sign new certificates with the private key of CA). Moreover mostly you need to have Root Certificate without private key on many computers and have the certificate with private key on one computer where you will do signing with the certificate.

I have encountered this problem and it seems that even the user with which you are running the FindPrivateKey tool does not have access to the key and therefore you would get the "Unable to obtain private key file name" message.
In the most cases you need import certificate with the private key in My store of some user and import in Root only certificate without private key. In the first part you generate a self-signed certificate which can be used as a CA certificates and you save it as rootcert.pfx file. I do tell the private key to persist in the CSP the problem is it doesn't It look like it.
In the second part you import the certificate, but use RSACryptoServiceProvider filled with properties of previous created key instead of using rootcert.pfx. You can also use MakeCert.exe to create other certificate which are signed with the CA certificate.

To be able to save information about the key container in the certificate store Microsoft introduced so named Certificate Extended Properties. If you don't tell the privatekey to persist it will only stay there as long as you application runs.
Moreover you can consider to remove private key directly after the usage, import it only if you really need to use it and not hold it permanently.

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