OK, your problem is that you're trying to feed these bytes into the ASN.1 decoder as-is. They are base-64 encoded. That's why you got the error message complaining about the APPLICATION 13 tag.The ASN.1 decoder expects the raw, binary, DER encoding. You need to base-64 decode the message before you try to decode the DER.
Note that the sample program in org.mozilla.jss.pkix.crmf.CertReqMsg does almost exactly what you are doing, except it doesn't have to base64-decode the message first. (http://lxr.mozilla.org/mozilla/source/security/jss/org/mozilla/jss/pkix/crmf/CertReqMsg.java#265) I don't think there's a way to base64-decode the data with JSS, but there's got to be some free code out there somewhere that does it. Or write your own!
