I guess I'd loosen the bolt/nut on the connection on the shaft under the van,
shift the shifter under the van at the transaxle into neutral, have someone hold that
back shift rod in place, then shift the shifter up front into neutral (it likely wants to sit
in neutral, toward the passenger side of the shift pattern, between 3rd/4th),
tighten the bolt and see how things line up.

Bentley has the procedure and this thread on Samba may help:
http://www.thesamba.com/vw/forum/viewtopic.php?t=294351

bob
On Aug 31, 2013, at 9:03 PM, Bruce Todd <beeceetee@GMAIL.COM> wrote:

Funny - I believe I am experiencing the same issue as of last night.  Went
to drive to a buddy's place and couldn't find first.  Eventually located it
over toward reverse having to push the shifter down - second is directly
below first and reverse slightly further to the left and up.  Third and
fourth seem to be where first and second typically sit.  The only gear that
seems to be in the right spot is my low gear (Syncro).

Had the shift mechanism housing off and inspected the shift rod and gear
shift union as well as the stop plates mounted to the inside of the housing
but didn't see anything blatantly wrong.