Can't tell what year bike you have, also how many miles/kilometers has the bike accumulated ?
You cannot get the clutch pushrod removed from the transmission with the swing arm in the way, it's too long to clear it .
How does the clutch pushrod bearing, that's the one under the rubber boot at the rear of the transmission look .
It's supposed to have lube on it, gear lube grease, it should not be 'dry' .
To remove the push rod without removing the transmission, you need to remove the swing arm .
The end of the pushrod, has a hole that's threaded, like some sort of tool could be inserted there then removed, by say something like a slide hammer, or puller .
It's a possibility that you may need a bit of grease on the pushrod where it contacts the diaphragm spring .