Arien524 when clutch is engaged the wheels donot pull right away

So if you raise the revs to say about 4000 rpm and let the clutch out does it stall or judder or both will it engage at all and pull away ?

It is possible that the throw out fingers have gone behind the throw out bearing housing causing the lever to be in the wrong position. If you can get an inspection plate off under the fly wheel you may see if this is the case . If not you may have to pull the box again

You may want to make sure the clutch cable is properly adjusted. At the clutch lever on the handlebars, pull back the rubber cover over the end of the cable where it goes into the lever. You'll find a round lock wheel that you tighten to prevent the clutch cable adjustment from moving. Loosen that wheel then you can turn the clutch cable adjustment in or out to adjust the clutch engagement and take up. For those bikes, you want to adjust it so that there is a small amount of slack in the clutch lever. Look at the "crack" where the lever pivots when you pull on it. Adjust the clutch cable by turning that adjustment in or out until you have just barely enough opening to slip a nickel edge into the very outside of that "crack" when you apply very, very light pressure to the clutch lever (just enough pressure to take the slack out of the lever). Tighten the lock wheel back into place and try it now. Also, make sure you are using a good, FIRM foot pressure to engage each gear. If you don't engage firmly enough or the adjustment is out, then it will pop out of gear. You notice it more on the lower gears because the lower gears allow the engine to send more torque thru the clutch, thereby providing more force to make it pop out of gear.

If this doesn't help, then take it to a shop to see if it's simple worn clutch disks (easy to replace on this bike) or if the gears have worn teeth in the transmission.

bad pressure plate or stuck throw out bearing.

Does the clutch not engage( ie it slips & wont pull away) or does it not dis-engage (ie always in gear)
Was the clutch dismantled or disturbed when top-end was replaced
Is clutch hydraulic or not

I'm not sure what you mean by "engage the clutch". If you mean when you pull the clutch lever, the noise goes away, I'd check the tension on my final drive belt. If the belt is loose, when the engine tries to slow the motorcycle down, the final drive belt tries to rise up off of the front belt pulley making it rub the underside of the starter to inner primary housing. When you pull the clutch lever in, you disengage the engine from the transmission and the engine breaking force is removed from the front pulley and the belt goes back down on the pulley.

Good Luck
Steve

If you select a gear without pulling clutch in it will grind and stall.
If you are certain the bike is engaging a gear and still seems it is in neutral, your clutch drive is broken.
Alternatively, the gear selecter fork bolts maybe loose behind the sidecover, allowing selector to partially engage only and return to neutral. Try selection thru' higher gears, place bike on a stand and turn back wheel in gear, if gears turn and motor doesn't...it is the clutch. If you cannot select a gear proper with rear wheel turning, your selecter is suspect.
Goodluck, and Cheers.

clutch slipping change the clutch

clutch needing replaced, very common on all manuals

pedal travel adjustment,yes
gear shift adjustment,no