I have a 1998 accord 4cyl coupe manual trans. The

A clutch issue youtend to have more of an engagement problem with 1st and reverse gear for a small time period before you notice other gears.You want to check the clutch hydrolic system for any leaks(clutch slave at transmission,clutch master,which you look for leakage on interior above clutch pedal)and at fluid resevoir.you also want to double check condition of trans fluid. strongly recommend using only HONDA BRAND MANUAL TRANS. FLUID when doing maintinance,fluid should be replaced every 30k on this car.The Honda brand fluid is like night and day on these cars,it WILL make a difference in shifting!!TRust Me on this point! Sorry now back to your main clutch issue,when driveing and you go to shift gears and normally notice grinding,with clutch pedal in shft out of gear and before engageing it into next gear do a double pump of clutch pedal then see if when continuing to next gear if it engagees smoother.if so you know you have without a dout a clutch pressure plate/disc problem. I can tell you that in twenty years the only manual transmissions themselves that ever had problems were due to outside influences(gear oil in transmission,improper driveing,etc.)let me know what you find and we can go from there..JOEL