Yes, the insert bushing can wear out. I have heard of instances of where people have reported that they had to change the insert or buy a whole new shifter assembly (can't remember if that part can be ordered separately, check with your parts dept). BUT you also have stated that there wasn't any noise before you installed the booger bushings. Which seems weird, at least to me, that any noice or vibration should occur. The insert bushing is generally changed IF there is an excessive amount of play or looseness noticed.
Like I suggested, take the whole shifter apart and regrease everything, including this time the booger bushings. Then see if that fixes your problem. I have changed or helped change many PT shifters and/or added booger bushings for many of my friends and never had a vibration noise problem complaint come up. The insert bushing is a split on one side bushing that surrounds the shifter pivot ball and actuator shaft. So take your time getting the insert off so you can grease the shifter ball, actuator rod/shaft, upper aluminum housing, and insert bushing correctly. Also the lower riser block, that big black plastic piece under the shifter, has locator pins molded into it, so make sure it's aligned into the shifter bracket when you put everything back together and before you tighten the bolts. I like to tilt the shifter so I can install the right side cable before putting in and tightening the bolts. The left side cable can be snapped/locked into place with just a large flat screwdriver or a 1/4" drive small socket and extension. Check the clearances around the cables and with the shifter in all the gear positions. Move the stick around when it's in a gear and see (may need a 2nd person) if anything hits. There is a possibility that the actuator arm was bent when you installed the cable on the left side, but you would have to check that.
The mistake many people make is not greasing polyurethane bushings, wherever they are used, and then forcing on/using them dry causing other problems. Is it more messy when you are using grease? Yes, but I don't plan on going back into or redoing stuff a 2nd time and covering your seats, etc is just a small price to pay.
If you have the extra cash, I would change/buy a new shifter, if I was taking everything part. The shorter shift is worth it to me. Can see the different short shifters available and their part numbers for the PT at my site,
http://sci-fi.ptenthusiasts.net/photo6.html , about halfway down the page. The B&M and Hurst shifters are the most popular and well known, but the OBX comes in different colors and the Pacesetter has a threaded shaft where you can adjust the shifter pivot ball up or down to change the pivot point and get the short throw you want/desire.
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