Have developed a noise when coming to a stop with clutch squeeze and in first gear

What exactly do you mean by 'trouble getting it to go into gear". Are you getting noises? If yes describe the noise. Is it 'lurching' into the next gear as you lift the clutch pedal?
Where was the smoke coming from? Smoking from the actual transmission housing could mean the clutch friction plate is contaminated with oil, possibly a failing crankshaft end seal. This can also affect gear shifting as the clutch will 'slip' as it tries to grip the flywheel.

Probably a bad clutch throwout bearing

Sounds like a release bearing is going bad.

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

Does the noise happen only when you pull in on the clutch (disengage the clutch), and go away when you let the clutch out (engage the clutch)?

If so, that's the clutch plates rattling until the spring load is reapplied to clamp the up.

A noise in neutral that goes when the clutch is disengaged indicates a front input shaft bearing in the gear box . When the clutch is out that shaft is spinning along with the cluster shaft in the gear box. When the clutch is in that shaft stops (to engage first gear) and the bearing is no longer working.. It normally means a box out job.

When you start the engine the clutch shaft into the gear box is spinning with the engine crankshaft. When you depress the clutch the noise stops because the input shaft is not turning. It points to a failing bearing on the clutch input shaft and if that proves to be the case then the box has to come out and be pulled down for the bearing to be replaced.

the oil pump went out

Where the noise is coming from?

Head of engine?
Centre of engine?

Do you feel that your bike is riding heavy that is you are forwarding the gears but the load of engine is not lightning.

Please reply me then i will tell you the solution.