Congrats on getting the car and congrats on getting a great color.

I have the notchy and clunky 2nd gear shift too. I'm going to try to change out the tranny oil this summer to see if it helps. It has helped other people's cars.

 

Since there are so many people that comment on the "clunk" and since both our '00 and '01 exhibit this when cold, I'd have to think this is normal. It does shift smoother when warm, it does shift better when you're at 5000 rpm +, but it does not go away with mileage. I'm no engineer, but I'm assuming that with the short throws and direct linkage, you cannot avoid feeling "something" One mechanic suggested that we are feeling the synchro not quite getting spun up to speed. This is why it is smoother at a higher rpm.

FWIW, my MR-2 felt the same way on a first to second shift. The "clunk" was improved with a switch to Redline MTL BUT I am not doing this to the Honda's till the warranty is up. I suggest you keep that in mind before switching fluid.

 

The jury is still divided on this - some say it's better, some say it's worse. Personally, I'd stay with Honda MTF.

 

Just adding my 2 cents.

Honda "improved the manual tranny in the '02". While I can atest to the fact that shifting is a bit smoother in my '02 than it was in my '01, I still have a bit of "notchiness" in my 1-2 and 2-3 shifts when the car is cold. After a few minutes of warm up and a few conservative miles, the tranny seems to smooth out. Just like my '01.