You do NOT need to "use" the transmission from the new "donor vehicle", this
requirement is frequently misunderstood when first reading the regs.

The transmission requirement is best summed up as this:
You can only put a new motor in behind an old automatic transmission
(Vanagon) if the new motor was offered in a factory vehicle (donor vehicle)
behind an automatic transmission
You can only put a new motor in behind a old manual transmission (Vanagon)
if the new motor was offered in a factory vehicle (donor vehicle) behind a
manual transmission.

Hence, if the new motor was available behind both it can be installed behind
either...  make sense?  So is there a Ford model out there running a Zetec
behind a manual?  and an Automatic? then your fine... if not... then in
California you can only put the Zetec in vans with transmission
configuration available.

It does not matter how many speeds the transmission has or anything else,
just automatic vs. manual.

The rational I believe is that the "emission profile" of an automatic is
different than a manual...  Seems trivial when your talking about installing
a 20 year newer motor, but that's the deal...

Now, where you might still run into trouble is with all the OBD II sensors.
If they are hooked into the transmission you might be screwed since I can't
imagine it being practical to retrofit things like that.  I think this is
why the Subaru's have to manufacture a speed sensor and hook it up to be OBD
I compliant...  Anyway, in the end you need to be able to run the motor
without generating any fault codes.  If you generate fault codes you won't
pass SMOG at a referee.  This screws up a lot of people that do Subaru
conversions...  You can, IIRC, get "permissible" fault codes put into a CARB
EO.   Kennedy might have done that on the Subaru's...  or maybe it was
Eurospec that did that...  I don't recall...

-Jon