Hmm, sounds very familiar.  I had an intermittent short
in a coil that acted just that way.  It would be fine again
once it cooled off enough. Well, except for that last time..
Sorry for not seeing your message sooner..

  Hey, I just put my engine back together and noticed I had
one spare small vacuum line and one spare vacuum port, but 
that none could reach the other.  I was wondering if you
could help me out.  I have one small line coming from 
the brake line vacuum on the other side of the firewall
connected to the thermal vacuum switch.  The other side
of that is connected to the EGR valve (I screwed up and
don't remember which line goes to the aluminum line and
which goes to the brass (any ideas?)).  I have two
small lines coming from the throttle body to the distributor
(these should be fine).  I also have one small line coming
from the front of the intake manifold going to a T
connected to the Decel valve above the engine with the
other end plugged (not right).  The free port that
needs a line is on the driver's side of the charcoal
cannister.  Can you decode this?  Where have I gone
wrong?

I'll post a message about why I pulled the engine after
tomorrow's highway test..

-- John