One key note is the clutch slave cyl is best bled when off the transmission. Air can hide away due to the angle it's mounted on the transmission. If the fluid is dark - it's likely it's at least part of the problem. It's easy to gravity bleed the clutch (just like brakes).
Just ensure you don't let the fluid res go dry - or you'll have to chase air out of the system.

Place plenty of paper towels around the master cylinder/fluid res to ensure any brake fluid spilled while topping off the fluid res doesn't get on any painted surface;
-Top off the fluid res (consider removing some of the old fluid first and replacing it with clean fluid);
-Unbolt the slave cyl from the trans (the actuator arm resides under the black rubber boot on the lower drivers' side of the transmission - note the slave cylinder's position when removing it to prevent having to play the "how did this go?" game when reinstalling it);
-Hook up a brake bleed line (clear vinyl tubing) to the bleed fitting and run the other end to a jar partially filled with clean fluid - ensure the line to the collection jar stays submerged in the fluid;
-Tilt the slave cylinder such that the bleed fitting is absolutely at the highest point;
-Crack the bleed fitting and run all the old fluid out until only clean fluid and no air comes out - ensure you keep the fluid res filled up to keep air from getting into the system - Gently adjust the slave cylinder position slightly to coax out any stashed air while you're doing this.
-Regrease the ball and socket (ball on the slave cylinder, socket on the actuator arm) and rebolt the slave cylinder to the trans. All done.

Some people will unseat the actuator arm and re-grease the pivot points (using a long screw driver or the like) while the slave cylinder is out of the way.

I use DOT4 fluid (ATE).

I would also change the trans fluid. If you still have issues after you replace the clutch fluid and the trans fluid - there may be other issues at hand.

 

There is a simple solution to Transmission issues.

Replace the MTF.

Check Clutch Fluid. Bleeding the clutch helps out a lot but the best thing to do is flush it and replace with Valvoline SynTech or some other high Dry/Wet Boiling Point fluid (RBF600, ATE Super Blue, etc).

If you still have issues it may be time for a new clutch/pressure plate.

Also, there can be other situations.

We had a client who put in the Toda 8lb Flywheel in his AP2.

He was having issues getting it into 3-6th and Reverse. When he brought it to us we found that the flywheel was warped possibly to production or improper install by the other shop. This caused issues with his clutch and pp.

 

I bought a Toda flywheel from King. I ran the Mugen PP and OEM disc with the setup. My car was basically stock at the time and I experienced a lot of slippage. I had the setup removed and replaced with a Comptech FW, ACT PP, and OEM disc and can't see the setup getting any better. I'm not a fan of Toda products.

Once again: The best thing to do is to change the Trans fluid and clutch fluid first - start simple.
After that you may want to look into whether the problem is with your clutch or transmission. If the car was abused previously, it could very well be a problem with something in the clutch system.
Which brings me to the next point: Anyone that buys a second-hand AP1 should always have the retainers inspected by someone who knows what to look for. A number of folks have had to learn that lesson the hard way - by having the engine eat itself up due to a dropped valve.

So if you haven't had the valve spring retainers inspected (by someone who knows what to look for - and that usually does NOT mean a Honda tech) you need to do it soon. Do a search under "cracked retainers" and read everything Billman has to say on the subject. He is without a doubt the #1 knowlege guru regarding most things S2000.

 

The motors brand new and the s2k was bought from a member on the board. I'll take it to honda to have the trans fluid changed as well as the clutch fluid. Hopefully if something is wrong, it's the clutch. I'm getting a inlinebro kit soon and will have to redo the clutch anyways.