There is a TSB (HSN 1003-06) that was released by Honda on October 1st, 2003 and applies to 1998-2004 Accord, 1996-2003 Civic, 1997-2003 CR-V, 2003 Element, 2001-03 Insight, and 2000-2003 S2000. It states the following:
If you're getting complaints that the M/T is hard to shift into 1st gear or that it grinds into Reverse, there may not be enough lubrication on the clutch disc spline. If the spline isn't lubricated sufficiently, the clutch disc can drag against the flywheel when the clutch is disengaged. This clutch drag is what makes it a hassle to engage 1st gear and Reverse when the engine is running, especially when the clutch and M/T are cold. To fix this problem and prevent it from happening again, apply a thin coat of super high temperature grease (P/N 08798-9002, H/C 3720984) to the mainshaft splines.
With this being said, I would start with the easiest thing to check which is the tranny fluid level. Put the car on a lift or on jack stands and make sure it is level. Remove the top bolt (I believe it is a 18mm bolt) and fill with Honda tranny fluid until it runs out from the hole). If the fluid level is correct then move onto the next step.
Check your shifter cables (under the hood) and make sure there isn't excessive play in the cable.
Judging by your problem, (which I had the same exact issue) I would highly suggest replacing the clutch. The information on the TSB listed above is the most likely culprit in your problem, and if you're going to go through the trouble of removing the tranny just to lube the mainshaft splines, you might as well replace the clutch and replace or resurface the flywheel. I just replaced the clutch on my car this weekend and made sure to use a light coat of heavy duty high temp grease on the splines and release fork. And the problem went away. Shifts are perfect now, where as before, I had your same problem. If you are going to do the job yourself, follow the sequence listed below:
-REMOVE BATTERY
-REMOVE INTAKE
-REMOVE BATTERY TRAY
-REMOVE ENGINE WIRE HARNESS CLAMP
-REMOVE SLAVE CYLINDER AND CLUTCH LINE CLAMP (DO NOT OPERATE PEDAL AT THIS POINT)
-REMOVE STARTER
-DISCONNECT BACK-UP LIGHT SWITCH CONNECTORS
-REMOVE TRANSMISSION GROUND CABLE AND STARTER CLAMP
-REMOVE CABLE BRACKET
-DISCONNECT THE VEHICLE SPEED SENSOR
-REMOVE ENGINE WIRE HARNESS AND TWO UPPER TRANSMISSION MOUNTING BOLTS
-REMOVE FRONT ENGINE MOUNT BRACKET 3 MOUNTING BOLTS
-RAISE VEHICLE AND MAKE SURE IT IS SECURELY SUPPORTED.
-DRAIN TRANSMISSION FLUID
-REMOVE SPLASH SHIELD
-REMOVE COTTER PINS AND LOOSEN CASTLE NUTS THEN SEPARATE THE BALL JOINTS AND LOWER ARMS ON BOTH SIDES
-REMOVE THE DAMPER FORKS
-REMOVE AXLES
-REMOVE INTERMEDIATE SHAFT
-REMOVE ENGINE STIFFENER (LOWER CLUTCH COVER)
-REMOVE POWER STEERING COOLER LINE FROM FRONT BEAM
-MARK AND THEN REMOVE FRONT BEAM
-LIFT AND SUPPORT THE ENGINE/TRANSMISSION ASSEMBLY
-REMOVE TRANSMISSION MOUNT BRACKET AND TRANSMISSION MOUNT
-REMOVE INTAKE MANIFOLD BRACKET
-REMOVE 2 REAR ENGINE MOUNT BRACKET MOUNTING BOLTS
-REMOVE THE REAR SIDE TRANSMISSION MOUNTING BOLT
-REMOVE FRONT SIDE TRANSMISSION MOUNTING BOLT.
-PULL TRANSMISSION AWAY FROM ENGINE AND LOWER AWAY
-REMOVE BOOT, RELEASE FORK AND RELEASE BEARING FROM THE TRANSMISSION
-REPLACE CLUTCH AND FLYWHEEL
-PUT THAT MESS BACK TOGETHER IN REVERSE ORDER
If you don't have the tools (including torque wrenches), confidence or experience, or time to do all of this (safely) then don't even attempt. If you are planning on doing this yourself, you are looking at an ALL DAY job without a lift.
HOPE THIS HELPS!
I forgot to list probable causes...
-LOW OR WRONG TRANSMISSION FLUID
-WORN OR DAMAGED CLUTCH AND/OR FLYWHEEL
-DAMAGED SYNCHRONIZERS
-TOO MUCH SLACK IN SHIFTER CABLES
-OR THE ABOVE TSB
There are a lot of other factors that go into a transmission but given the fact that it only happens in first gear (and in reverse as is the case with Redlinevtec) then the other **** is irrelevant.
