The problem is the first command, you are creating a self signed certificate and adding it to the Trusted Root store of the Local Machine account (but you probably know that). But you're also creating files for the public and private keys for the certificate, the .pvk and .cer files.
The second command is creating another certificate, this time not a self signed one but signed by the first certificate. In order to sign a certificate you need both the public and the private key of the issuer (CN=MyCA), you are instructing makecert to look for the issuer public key in the Local Machine Trusted Root Certificate store, that's fine, but you don't have the private key anymore, since MyCA.pvk was deleted.
If you don't specify file names for the private and public keys on the first command, i.e. do not include the -sv MyCA.pvk parameter and MyCA.cer, both the public and private keys will be added to the store. That means there will be no need to delete files because they won't be generated.
Also, if you open a management console, press [WIN]+[R] type mmc [Return], go to File -> Add/Remove Snap in -> Select "Certificates" -> "Add" -> "Computer Account" and then navigate the tree to Trusted Root Certificates\Certificates you will find MyCA in the left pane. You'll notice a small key on the icon and if you double click the certificate a message at the bottom of the General tab properties will state "You have a private key that corresponds to this certificate". That means you can use that certificate to sign a new one, like you're trying to do in with the second command.