If you don't jumper as directed, then as you try to adjust the timing by
rotating the distributor housing, the engine control system will
simultaneously attempt to undo what you do.

At whose diagrams are you looking?

Try this drawing for a 97 Civic DX (which looks a lot like the 96 and 98
Civic LX drawing):
http://www.hondaautomotiveparts.com/auto/jsp/mws/prddisplay.jsp?inputstate=5
&catcgry1=Civic&catcgry2=1997&catcgry3=4DR+DX&catcgry4=KA4AT&catcgry5=BREATH
ER+CHAMBER+%281%29

Note the "Front" direction arrows on the drawings. The "breather chamber,"
to which the PCV valve connects, is something like 4 to 6 inches by 4 to 6
inches, about an inch thick. Painted black.

I couldn't get an LX drawing via this site, but www.slhonda has a drawing
for the 97 civic lx that looks like the above.

It also helps having a new PCV valve in your hand, matching it to what you
see under the hood.

On the other hand, I think someone posted here in the last couple of years
that getting at the PCV valve on his late 1990s Honda was a pain. I think
the poster said he had to get at it from under the car. From the drawing,
this might be one of those Hondas. Take a flashlight with you, or make sure
the sun is shining on the top of the engine when you check.

By contrast, people talking about early 1990s Hondas will report it's easy
to get at (from the top, with little in the way to remove it).

if you leave it unconnected when you run the timing light, you'll see
the timing mark jump about as the ecu varies timing.  with the service
connector shorted, it holds the timing steady so you can set it right.

just keep checking for the pcv.  it /will/ be there.

When you set the distributor, you are setting the "base" timing, which is
the datum from which all other adjustments are made. This floor must be
correctly set, otherwise everything else may be off.

Jumping that connector prevents the ECM from being able to adjust the
timing while you're setting it, so you are for sure setting the "base"
timing without interference from the computer.

It is not a given that the ECM will adjust the timing, but if it does, your
base setting will be messed up.

You mean the OBD connector?
http://www.tegger.com/hondafaq/faq.html#retrieve