The pushrod slides part way into the rod inside the engine case, if you insert it slightly off square then it catches the outer lip on the other half and doesn't fully insert, a bit of a jiggle usually gets it to go in all the way.
With regards the slave cylinder, the piston tends to creep, I find it best to depress the slave piston fully with my fingers and then assemble it all as quickly as possible to get both bolts engaged square without load on the pushrod.
Best of luck.