I switched to a 90 CRX Si tranny in my 89 DX hatch. I used the 90 Si clutch, pp, and flywheel which had less than 100 miles on them. Whenever I downshift from 3rd to 2nd or 2nd to 1st I hear this noise and I can feel it in the shifter. It's not a grind but more like friction from something rubbing. It's kinda like brakes grazing the rotor or something. It will do it even if I'm in 1st and letting it hold me back going down a hill at 5-10 mph. I'm wondering if the synchros could be going bad? I haven't had tranny problems before so I have no idea what the problem is.

 

could be the syncros starting ot let go. usualyl if they are crap it'll grind in and out of gears. some si trans are just noisy. mine is quite noisy when going from 3-2 or 2-1 like yours. however it doesnt vibrate or grind or anything. just noisy syncros.

 

Mine is very noisy as well. Keep in mind these are 13+ year old pieces of hardware we're talking about here... I'm sure if you invested in a complete tranny rebuild, it might smooth things out a bit. Either way, I'm sure everything is okay - synchros couldn't function without friction, so your tranny seems like it's just doing it's same old tired job...

From the way you described it though, it actually seems much healthier than my tranny! ('90 Si as well)