All I know is that there have been quite a few guys who have done this
conversion and I have never heard any of them complain about passing
emissions.  If the motor is running properly and a Catalytic converter is
installed I think that you will have no problem with emissions.
As for cost, the conversion is cheaper including the work, than slapping down
$3000 for the dealer (usually the only person in the area willing to do it) to
change out your motor with a rebuilt one.  The Vanagon tranny can handle the
conversion as it has been engineered to take up to 300 hp (I have read this
somewhere).  The only thing I would recommend is upgrading the clutch to a
stronger one and maybe welding 4th gear.
As for shops not willing to do the work, I don't know any good shop that
hasn't done some type of conversion some time in the past whether it was a
Chevy V8 into a Porsche or Jaguar or a Corvair engine into a Transporter.  You
just have to be sure to find a good shop with a mechanic that is willing to
work by the hour and likes the challenge of a conversion.
I am happy for you that your van has been running good for so many miles, but
when I get letters from guys who have replaced their motors time and time
again and are at their wits end as to what to do, I feel obligated to offer
them an alternative to what I feel is throwing money at a problem instead of
trying to solve it.
Thats my 2 cents.
Ken Wilford
John 3:16