Please help quick...

[Eddie <axr11@po.cwru.edu>]

Well-I took my car into the dealer two thursdays ago since i was having
trouble shifting into first, it was making crunching noises when i stuck it
in reverse, and the clutch was making weird noises. so they told me to
bring it back in on monday since they said the transmission needed to be
rebuilt. it seems extremely odd that something like this would happen after
35,500 miles. but i did bring it back, and i finally got it back tonite
after a week of it sitting in the shop (they were ordering parts, tools,
blah blah, and it was taking a while because they had never seen a problem
like this before...). 

they told me that what happened was that a tooth broke off the reverse gear
and was bouncing around in the tranny and messed up the other gears. they
said they had fixed this problem, and when driving the car out of the
parking lot, i could feel that 1st and 2nd gears were very stiff and not
the typical feel we're used to. so i brought it right back around, and one
of the techs drove and said that something was definitely wrong. in the
meanwhile, as soon as i started my car, the check engine light also came
on. then the tech hooks it up to his computer to check what the check
engine light was about, and he managed to get it turned off, but said there
was a 99% chance that it'd come back on again on the drive home, and that
it was a "hard fault" now permanently stored in the computer (whatever that
means)- hopefully something simple like an air intake problem, or maybe a
loose sensor because of the transmission work. in the meanwhile, i'm
thinking in my head that it's hopefully not the garrett chip i put in. and
i'm scared that if he figures out that there's a chip in there, he might
void my engine's warranty (even though there's only 500 miles left...).
accordingly, i tell him i'll drop it off again in the morning so that if i
decide to, i can take the chip out. my question is this: what are the
chances that they'll know there's an after-market chip in there, and is
there a possibility that that might be the problem? i don't want to mess
with the chip at this point because i didn't put it in myself, and i know
it'll take me hours including time to go buy the right tools to take it
back out. in addition, when the manger heard there was another problem with
my car, he came out and said he would look into the problem himself
tomorrow morning. will they have to look in the ECU to figure out what's
wrong? and will their computer instantly tell them that it's an
after-market chip? the light had come on once about 1000 miles ago for
about 2 seconds, but nothing since...

thanks in advance...any answers/comments will be greatly appreciated...
-Eddie '99 Jetta VR6 (A3)