I have a 2000 Wrangler with a 4 liter and manual five speed.  I'm the second
owner and the first owner was a nurse that used the jeep as a highway
commuter car.  The jeep has not been wrecked, rolled, or ever stuck.

Over a year ago the reverse lockout pin was found (broken) while changing
the transmission fluid.  I took it to the dealer under warranty and they
rebuilt the transmission.  However, as soon as I picked up the Jeep there
was a shift problem. That's when upshifting into 2ndfelt like a tooth or two
was grinding past.  It would shift and stay in 2nd gear, but it was like the
clutch was only partially depressed while upshifting - like a lazy upshift
micro-grind.  Shifting up to 3rd had a similar feel, but was less
noticeable.  Downshifting was as it should be.  No grind, but smooth
shifting.

So, I took it back of course.  They tried a number of things, including
rebuilding the transmission, clutch, throwout bearing, etc.  Nothing helped.
And after five overnight trips to the dealer (30 miles away) they told me
there was nothing they could do.  When they test drove it, it was like they
were driving the Pope-mobile and they would always take about three seconds
to shift from one gear to the next - and with that time lag, the problem is
less noticeable - but I could still hear it from the passenger seat.
However, that kind of shift is not normal or comfortable.  I didn't throw a
big enough fit and the warranty eventually expired.

The problem stayed and eventually got to the point of occasional full
fledged grinds when shifting into second.  Before having a lift put in the
Wrangler I wanted to be sure the transmission was going to be good for the
next 50,000 miles or so, so I took it to a one man transmission shop that
was recommended by a long time general automotive mechanic I have known for
years.

He couldn't find anything really wrong with the transmission except a little
abrasion on the shaft - and he replaced the shaft.  He thought the dealer
had been using the wrong fluid and initially the transmission shifted better
with the fluid he used.  However, after only about 1,000 miles, the shifting
problem (not the all out grind) is back.

Unfortunately, while it was shifting better, I had a lot of work done on the
Jeep.  Now I have a 4 inch lift, new tires, new differentials, and new drive
shaft, but the transmission is annoying as hell.  I can shift REAL slow, or
double clutch when going up to 2nd, but that's not a cure, there is still
something not meshing like it should.

So, finally, any suggestions?  I've even starting thinking of a new
transmission, but the wife is going to kill me if it comes to that.

Masnor@cox.net