I have a 2000 Civic EX and I recently put new poly shifter bushings in it, and a short shifter. directly after installing the shifter I started getting a weird knocking could feel through the shifter when it was accelerating in low gears. I made sure everything was tight and I was under the car and had someone run through the gears checking for clearance issues, nothing. Everything seems to be in working order. The noise and knocking seem to go away once the car gets up to speed in higher gears (3, and 4). Any ideas on what else it could be?

 

Double check your work, yeah you said you did it but I'm still going to recommend it.

 

Some short shifters will hit the exhaust piping and will rattle on decell depending on what short shifter you are using and shift linkage.

What brand short shifter is it?

 

Mine is a b&m short shifter and mine rattles I was wondering is there is suppose to be a rubber bushing or washer where you bolt the shifter to the linkage? Or is it metal to metal contact...

 

You could also have a bad motor or transmission mount causing the vibration issues to amplify into the shifter linkage

 

I have the straight B&M short shifter and the poly bushing on a b16a in my 93 si and it makes a rattling noise, although I got a slighlty heavier shift **** and seems to have gone away mostly, I planning to replace with a skunk2 single bend and shift ****, so I will see at some point if it makes difference

 

mine is the same too bro I feel your pain lol. It gets annoying as hell.