Harley troubleshooting idling in neutral the bike has developed a rattle behind the primary cover. When I put the transmission in gear, the noise stops

You have a problem because a Harley rattles??? That is like saying you have a problem with English bikes leaking oil.

Older 4 speed transmissions were known for their "clunk" going into 1st gear.

However, even though you didn't give a model year, I'll assume you mean something newer than those.

If it "grabs" when going from neutral to 1st (bike wants to "jump"), it usually means the clutch push rod (under the primary cover's "Derby cover) needs adjustment, followed by the clutch cable.

As far as the leak where the cable enters the transmission, there is an "o-ring" seal that might need replacing.

Dont run your bike. Drain the primary/transmission fluid and remove the primary cover. If you dont imediatly see the problem put the shift lever on the shaft and put bike in gear by gently rocking back and forth. If you still dont see the problem it depends on the year your Sportster was made. If the noise is indeed comming from the left side (primary side) you will see what is hitting what and making that noise.

it could be a wrist pin, and im not sure if those amc's had hydraulic lifters but sometimes with old lifters when the oil pressure is lower at an idle the lifters arnt filling up all the way so they develope a little valve lash, and when the rpms are raised the oil pressure raises and fills the lifters. you could try chasing the noise down with an automotive stethoscope.

Have you checked the oil in your transmission. Look at the chrome end cap on the transmission. There's a large plug that takes a hex key or Allen wrench to remove. Take this plug out and there is a dipstick on the plug. Check the oil level with the bike standing straight up. The level should be between the two lines. The transmission holds 20-24 ounces of lubricant. Your bike came from the factory with H-D Syn3 20W50 engine oil in the engine, primary case, and the transmission. Also check your primary lube level. Stand the bike straight up and remove the derby cover. The oil should be to the bottom of the outer clutch drum. Do not overfill or the clutch will drag making finding neutral with the engine running almost impossible.

Good Luck
Steve

If your engine is running with the clutch out and you pull in the clutch and put the transmission in first gear, you'll hear a clunk, this is normal. The reason is that although your transmission is a constant mesh transmission it is not a synchronized transmission. I don't know of any motorcycle that has synchronizers in the transmission. When the engine is idling in neutral with the clutch out, the gears and shafts in the transmission are spinning. When you pull the clutch in, wait a second or two for the spinning transmission components to slow down or stop spinning before you kick the transmission into low gear. The hotter the transmission is, the thinner the lubricant in it and the longer you need to wait.

A clunk is normal but if the bike trys to pull forward and you have to hold the front brake to keep the bike from moving or you cannot find neutral with the engine running, you need to adjust the clutch. To adjust the clutch, find the rubber bellows in the middle of the clutch cable. Slide the bellows up and break the locknut loose. Shorten the cable as much as possible. Remove the derby cover from the left side of the primary cover. In the center of the clutch assembly, you'll see a clutch release rod adjustment. Break the locknut loose and adjust the center bolt inwards until a resistance is felt. Do not force the bolt, just until a resistance is felt. Back off on the bolt 1/2 to 1 full turn and lock the nut. Replace the derby cover and adjust the cable so that you've vote about an 1/8 inch of freeplay at the clutch lever. Lock the lock nut and replace the bellows. Good Luck, Steve

Make sure you do not overfill the primary. when putting the oil in the primary, have the bikes standing as straight up as possible. Add oil only until it comes to the bottom of the clutch spring. If you put too much oil in the primary, the oil will get in between the plates when the clutch is released and act like the oil in a automatic transmission torque converter. It will continue to drive just enough so that you cannot find neutral with the engine running.

Otherwise, you must make sure all clutch adjustments are correct. Loosen clutch cable all the way. Adjust clutch release adjuster behind derby cover, all the way in and back off one half to one complete turn, readjust cable for 1/8" freeplay.