RM 250 Knock....Clutch???? I need advice.

Sounds like bearings or piston slap, not the clutch. A misadjusted clutch is going to slip even if it's brand new. When you engage the clutch it is lightly loading the engine so whatever parts are worn and have excessive clearance don't have as much 'room' to accelerate so they don't make as much noise when they suddenly stop. Same principle applies when your riding - less noisy when there's a load on the engine. Without actually hearing it, it's hard to pinpoint what's causing it.

I wouldn't run the bike anymore. Time to tear the thing down, do the top end and measure/inspect everything else. If you don't know the maintenance history of the bike, I'd go ahead and change the crank seals and water pump seal while I was at it. If you continue to run it in it's current condition, it's a matter of time before the engine completely Chernobyls on you adding hundreds to the cost of repairing it.

If you plan on doing the work yourself, get a service manual. If you haven't done much work on bikes, I would suggest a Clymer's manual because they cover a lot of basic information, substitutes for some of the specialized tools, and have lot's of pictures to help you along. Factory service manuals assume you already know what you're doing therefore, don't contain much general information, but will have more specific information.

Could be running a bit lean, I would start with adjusting the jetting. It happened to mine until I richened the mixture

The 2000 RM250 I purchased earlier this year would fire up first kick. In addition, the compression was about 180psi. I tore it apart to do the top end just so I would know how many hours were on it. I found the piston was trashed, the cylinder was trashed, the head was trashed, and the crankshaft had a bad journal though the bearings were OK. Oh, and the bike wasn't making any noise.

I doubt that it's a jetting problem. If it were, I'd expect the noise to be louder under load. You could go ahead and check the plug to be sure.