Heh heh heh, he said nipple. How old are you and you don't know how to raise a nipple?

The pins that you speak should've been pulled by whomever machined it and then reinstalled, this may very well have been the case but he re-installed one a little on the deep side. The cylindrical thing that you speak of sounds more like the monotester sensor than an engine speed sensor. If it is the monotester pick up then that is what those pins are there for they are what the sensor reads to give an RPM signal. If this is the case then do not worry about it. The engine speed senor fits into the very top of the back of the block and there should be a big notch in the top of your bell housing to accomodate it. If your car is LH2.4 you will see a series of holes drilled into the edge of the flywheel, these are what the sensor uses to read off of. On a flexplate there would be a tin shield there with windows all the way around the circumference of the flexplate with on long blank space that the control unit uses to indicate TDC. In an LH 2.2 or earlier car all of this stuff is mounted into the distributor and is timed off of the cam shaft. So if you have an an LH 2.2 car then don't sweat it if it is an LH 2.4 car then make sure that it is timed properly.

Mark