Got a replacement engine which appears to have done very few miles and is a late model version.

It is very clean and good condition but has a dent in the Timing / genny which has caused a crack when you look at the inside of cover near the genny windings.
so I fitted my old engines genny cover.

The old genny cover wouldn't go on properly and when I investigated I discovered that the later engine has a a triple cog with tiny clutch plates between the toothed cogs. Because of this I fitted the old cover with the old standard cog fitted.
Result the starter doesn't turn over the engine. Just get the decompressor operating followed by a click and a faint whining noise.
Had 2 quick tries and decided to leave lest it wreck the starter.

Is anyone familiar the set up for the newer type starter cogs?
Is tharere a way I can get around this so starter will turn over engine.

Info:-
bike can be pushed along in gear and engine turns over fine.
The decompressor is also working fine.
Bike has a brand new battery fitted which is fully charged.

What year was the original engine, and the new?

I fear the difference between the old style and new style starter mechanisms completely prevents any compatibility. The addition of the clutch mechanism in the new style was in answer to the problem of the old starter and gears tendency to backlash and break the starter motor from the crankcase.

Sad to report that I know of no work-around to make the parts you have work together; and it sounds like you are now in the market for a late model left side engine cover. Probably best off to use the newer "clutch" system anyways and save your crankcase from possible future damage. Brand new left side crankcase cover is about $75 from Ron Ayer's.

That was a long time ago when I did search the differences.
Look up the illustration at Ron Ayers for a '86/ '88 and a year after '96
The gears are a set, meaning ALL are different, the small gears and the larger gear behind the rotor.
Conclusion: you need a cover from a '96 or later engine....

The new cover will be bare.
You need the following parts:
Gasket
Oilseal, the one that's inside and goes over the crankshaft, impossible ro remove undamaged.
Small o-ring of the clutch actuating shaft.

Note the position of the small starter gears and where the washers go.
Greetz