Raj... This is usually a sign of the ratchet pinion teeth jamming on the kickstart quadrant because the pinion teeth are worn. Although the box was rebuilt, it may still have parts with enough wear to cause this problem. The ratchet pinion should not bind on the mainshaft bush, which should also be a nice snug fit on the mainshaft. Like Musky says, wear here alters the geometry. The pinion must be free to move along the mainshaft bush to disengage the ratchet. Check the quadrant is the right one, with good teeth, (the first tooth is relieved to aid engagement) the pinion teeth are not worn, and the circular spring in the ratchet centre is good and has the spring supporting washer in place on the mainshaft bearing.
As a basic test, with the clutch disengaged, with hand pressure the pedal should move down with the same resistance through its arc of travel, smoothly and with no tight spots. The upward return under the influence of of the spring should be the same, with a regular click from the ratchet teeth.
Swarfy.