Alright. Here's the deal. i have a 99 Si with a b16a2. the motor has basic mods (intake exhaust fuel system hondata stage 3 clutch and flywheel). my tranny started to grind in third a couple weeks ago and i know it is my synchro. but then it makes a grinding type noise whenever i start to move in first. so i drained and refilled the tranny with fresh fluid because the old stuff was dark gray. (guess it wasnt changed when i got the car) anyways i changed the fluid about 2 or 3 weeks ago and and the grinding went away. so yesterday i checked the fluid when i changed the oil. the fluid is nasty gray again. i think it may have something to do with the master cylinder but i am not sure. i dont know but it is making me mad!! !

 

Sounds like you are eating away at your tranny! get some syncoro esh and see if that helps.