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The biggest things that affect shifting besides mechanical wear, are clutch hydraulics, and transmission fluid.
Is the clutch engaging high, or low in the pedal stroke? A low engaging clutch means a clutch release issue. A high engaging clutch and hard shifting means you should check your transmission fluid.
Honda's 3 year 36,000 mile transmission fluid change interval is way off the mark in my opinion. It should be changed yearly at least.
The symptoms you describe are indicative of clutch not fully disengaging. Very common on our cars.
First step, clutch rod adjust. Excellent diy youtube video how to. Only tool needed is 12mm open end wrench, and a nimble back to worm down into footwell.
If you know the fluid is low, I would not touch the clutch rod before I fixed the leak. I have had to replace a MC and a clutch on this car and have never once adjusted that rod. If it is set properly and no one has messed with it then it likely does not need adjusting.
To clarify, since this always ends up getting confusing to at least one person in the conversation, engaging a clutch is when you release the clutch pedal (car is moving) and disengaging is when you push the pedal.
If you have to push the clutch almost to the floor before it starts to disengage then that very often can be air in the system, very low clutch hydraulic level, a bad master or slave cylinder. And on this car, it does not have to be almost dry before it affects clutch disengaging and if bad enough it will not fully disengage and will make it hard to shift when the engine is running (but not when the engine is off). My MC started leaking at an autox event, when it got ways below the top fill line (maybe an inch or so), I noticed it in that it barely would disengage the clutch. Kept topping it off (which immediately brought most of the pedal back minus a bit of air that got in) to get me through the event and home so I could fix it.
If the clutch were never engaging fully, or disengaging very high in the pedal travel, then that more likely indicates a badly worn clutch. As the disc gets thinner, the pedal has to be further out for it to contact the flywheel. It could also be a very out of adjustment clutch rod, but if that is properly adjusted to begin with you really should not need to mess with that much.
If when pressing the clutch pedal, it seems pretty weak until the very end where you feel it starting to do something (disengage) and you see low fluid, I would find the leak first. If fluid is gone, it leaked and you need to fix that either way. It is likely sucking air from the area that is leaking and thus causing poor disengagement. Look VERY close under the MC. When mine leaked, it leaked a lot throughout the day and I did not see a drop... until I jacked up the car and it started pouring out of the plastic undertray beneath the driver side. It had run down the firewall and was ending up in there which made it hard to see on a quick glance. So try to find where it is leaking and fix that, then bleed the system well and see if the issue returns.
Clutch dust is not the cause, it doesn't mix with the fluid. The clutch fluid gets trashed faster because of frequency of use combined with length of travel (brake gets a 10th of the use and a 1/4 or so of the travel)
But yes a simple fluid swap (just suck out/wipe clean/refill) and it will never leak. It even stops over 90% of leaks in currently leaking clutch master cylinders. Many see a leak and change the master for nothing.
I've also noticed when the action of the pedal doesn't feel as smooth, suctioning out the old stuff and adding new stuff works to free-up the action.
I've been using ATE Typ 200 (yellow) in all my cars (brake and clutch hydraulics). Good stuff!
Looking at my blown out slave, it's amazing how little the seal needs to wear out to render it useless. Looking at it closely the unit experiences a fair bit of friction, the metal part of the piston has burnishing. About a tenth of a mm was worn off the rubber seal.
I would imagine an ungreased dried warped release guide creating extra hydraulic effort to release the clutch doesn't help.
If you know the fluid is low, I would not touch the clutch rod before I fixed the leak. I have had to replace a MC and a clutch on this car and have never once adjusted that rod. If it is set properly and no one has messed with it then it likely does not need adjusting.
To clarify, since this always ends up getting confusing to at least one person in the conversation, engaging a clutch is when you release the clutch pedal (car is moving) and disengaging is when you push the pedal.
If you have to push the clutch almost to the floor before it starts to disengage then that very often can be air in the system, very low clutch hydraulic level, a bad master or slave cylinder. And on this car, it does not have to be almost dry before it affects clutch disengaging and if bad enough it will not fully disengage and will make it hard to shift when the engine is running (but not when the engine is off). My MC started leaking at an autox event, when it got ways below the top fill line (maybe an inch or so), I noticed it in that it barely would disengage the clutch. Kept topping it off (which immediately brought most of the pedal back minus a bit of air that got in) to get me through the event and home so I could fix it.
If the clutch were never engaging fully, or disengaging very high in the pedal travel, then that more likely indicates a badly worn clutch. As the disc gets thinner, the pedal has to be further out for it to contact the flywheel. It could also be a very out of adjustment clutch rod, but if that is properly adjusted to begin with you really should not need to mess with that much.
If when pressing the clutch pedal, it seems pretty weak until the very end where you feel it starting to do something (disengage) and you see low fluid, I would find the leak first. If fluid is gone, it leaked and you need to fix that either way. It is likely sucking air from the area that is leaking and thus causing poor disengagement. Look VERY close under the MC. When mine leaked, it leaked a lot throughout the day and I did not see a drop... until I jacked up the car and it started pouring out of the plastic undertray beneath the driver side. It had run down the firewall and was ending up in there which made it hard to see on a quick glance. So try to find where it is leaking and fix that, then bleed the system well and see if the issue returns.
We tend to beat engine oil to death, maybe we can start with hydraulic/brake fluid!
We all know the "blue" in blue went away due to the nanny government so the clear/yellow is all we get. I have been using ATE SL.6 and it seems to work as advertised. I don't track so I am not concerned about the slightly lower boiling temp. It does make the anti-skid vibrate faster than the old Honda DOT 3 fluid. Most newer European cars with the magic VSA/AS/etc all use this stuff. It is made for this and if you have an AP2 with VSA, why not?
I have not used it in the clutch as it is not as easy to drain but I might.
update: flushing clutch (brake) fluid 4 times with turkey baster method and topping off to correct level appears to have fixed the problem. shifted effortlessly into reverse and other gears afterwards. used ate typ200 (DOT4)
can anyone explain to me why this system can lose fluid simply because the fluid is dirty —have seen credible folks mention this low and dirty fluid before flush dirty fluid
I don't think it is fluid loss that effects the pedal movement, when the fluid is dirty. The dirty fluid changes the smoothness of the action of the seals traveling through it. Makes the action "stickier."
