Here's a summarized version of what I've collected from "Woodwork" on the subject. (long) I have a notchy 3rd, that is improving with age but still comes back enough to be annoying - even with light shifting and attempting to place it precisly into 3rd.

SHIFTING TECHNIQUES
Woodwork (Honda engineer): Interesting thought, shifting from the side vs. shifting from the top (some forum members felt they had better control with their hand on the top of the shifter knob.)
If you let the detent spring take the shifter back to the 3-4 area of the neutral line you will always know where you are in the shift pattern. Try it. push it to the 1-2 area and it will always go back to the 3-4 rest. Same w/5-6. A light touch of the shifter might give you a better feel.

CARE & FEEDING OF 2ND GEAR SYNCHROS
Woodwork (Honda engineer): I am writing this to hopefully help S2000 owner/drivers understand the importance of shifting properly to minimize the damage to 2nd gear synchronizer rings. My overall objective being in the woodwork is to keep S2000 owners from hurting themselves and hurting their cars. Everytime a transmission or engine gets replaced in an S2000 I get the part. I've seen a lot of damaged transmissions. Before flaming me please read this and keep an open mind.
You have an engine that revs to 9000 RPM. That means that the transmission mainshaft and clutch disk are also revving to 9000 RPM. When you disengage the clutch (push in the pedal) to shift from first to second the engine and the transmission are disconnected. The engine will slow down from compression when you lift off the throttle. The mainshaft of the transmission is not connected to the engine any more so it is freewheeling in the transmission. Given enough time the mainshaft will slow down but not as fast as the engine. The countershaft is connected to the rear wheels and the speed stays constant during the shift. When you shift into 2nd gear the synchronizer of the 2nd gear must SLOW DOWN the transmission mainshaft to match the speed that the engine WILL be going when the shift is completed and the clutch is engaged. The transmission mainshaft and the clutch disk together weigh 19.75 lbs. (not including the pressure plate and flywheel that are connected to the engine) When you shift from 1st to 2nd at 9000 RPM the engine speed drops to 5900. That means that the little brass synchronizer rings have to push on the 2nd gear to slow the mainshaft from 9000RPM to 5900 RPM. It not only has to slow down the mainshaft it has to do it in the time that it takes you to shift. So if you have a tendency to shift fast you may be making the sleeve blow past the synchro rings before it has a chance to do it's job and it will smash into the 2nd gear.

The early '00 cars needed a little change to the sleeve to make the synchros work a little harder. That is what the new parts in the service bulletin are for. Cars after VIN VT006255 already have the new parts. Grinding in a car produced later than 6255 is possible if the synchros have been damaged and now are not able to slow down the mainshaft properly.

Shifting without the clutch, or, shift too quickly and not letting the synchros do their job may permanently damage the gear, sleeve and synchros and make the 2nd gear grind more often. It makes sense that if shifting at 6000 makes the engine speed drop to 4300 RPM, (1700) into 2nd gear then you should give the 2nd gear synchro twice the time to do the shift from 9000 RPM. If your car does grind once in a while you may not want the transmission removed, disassembled and a new 2nd gear put in. If it does it quite often, show it to the dealer and have it replaced.

If you hesitate for another 1/2 second while putting constant pressure on the shifter while the 2nd gear synchro does it's job, I'll bet many of your cars would not grind any more. Try it. You might like it.

TRANSMISSION PROBLEM WHEN COLD
I have a 2000, I had the TSB's done, no more grinding! (that was at 12K miles) now at 20K I can't get the car in gear when it's cold outside!
Woodwork (Honda engineer): It sounds like the clutch is not fully coming disengaged when it is cold.
Try this: When you experience the problem, turn off the engine and see if it goes into gear easier. If it does then it is the clutch. The other thing you can try: With nothing in front of the car (in a level parking lot) with the engine running open the door and take your foot off of the brake. Now when putting the shifter into 1st watch the ground to see if the car creeps forward any. If it does then the clutch isn't fully disengaging. The only way to fix this is to take the transmission out and clean the splines of the mainshaft and clutch disk. The problem is that if the splines are dirty they get cleaned off when the transmission comes out which destroys the evidence of dirt/etc on the splines.

 

My VIN ends in 6291 and was delivered to the dealership the last week of March 2000.
The xmission grinds from 1st to 2nd at random ... and I have never had the engine at 9,000RPM ... NEVER. The car was at the dealership for a week nearly a year ago to have a TSB done to modify the transmission. I have an invoice to prove it. Nothing changed. The car may go for weeks w/out a grind and then do the grind thing several times in a row .. not necessarily during a higher RPM shift (but never near 9,000RPM) ... once it did this in a slow and deliberate shift at 20MPH!!! ??Since my VIN is higher than you indicate, Woodwork, then why did the dealer modify the car or keep it a week and give me an invoice indicating they did???
Frankly, with nearly all of us paying over MSRP for this car, Honda needs to do the right thing and replace the transmission before this car winds up as the feature of a television investigative report! This is not the only fault of this vehicle.

 

Feels totally normal

The lurching forward does not happen all of the time so if the spline was dirty wouldn't this cause the car to lurch all of the time? Besides, I noticed an occasional lurch since new.


John