Does the shaft feel loose but is sticking in the valves? Sometimes it needs a little persuasion.

Can you pack some big washers behind the tool to assist on pulling the shaft out further?

If not..........

I gently persuade it by grabbing the end of the shaft in the (soft jaw) vice and tapping the cylinder, while of course holding the cylinder. Be careful to avoid bending the shaft. It's a bit Neanderthal but gets it done.

And yes, it's an E-clip.