I should preface the comments below by saying that I have never crossed the US Mexican border so cannot claim any first-hand knowledge, but hopefully something I write might be helpful...

1) What do you mean by a "second permission", do you mean a waiver or something? And the bike entered Mexico previously with an expired rego? That doesn't seem to make sense, presumably the previous US owner had a valid rego when he left the US?

2) As far as the US refusing you entry: not sure if that is the case; not all US states allow rego renewal online, and given how long the bike has been out of the US, it is understandable that the rego is expired. And I'm pretty sure I've read elsewhere on HUBB that people have entered the US with an expired rego and then rode straight to the nearest DMV to renew it. Even if that fails, as someone else pointed out, you should be able to truck the bike from the US border, because rego is only required to operate the vehicle on the roads, not to own it.

3) Have you asked these questions or for help on ADVRider? Given its American-heavy member base, I would think that a lot of them would have lots of Mexico-experience and might have some good advice. You might want to go the the appropriate geographic subforum and ask there. If nothing else you might find someone with a truck to pick you up at the US border.

Good luck, sorry to hear you're having such trouble with paperwork!