basics.. if it cocks fine without the stock, but not with the stock, then (wait for it) - it's the stock or fitment thereof stopping it cocking.
Have you tried cocking it without the stock fitted ? It takes a bit of strength and technique on an HW35. I lay the action upside down on a towel on a bench, with an end stop, and you can then use both hands for good control.
If the stock is indeed causing the problem, check easy stuff first.. is the latch definitely actually hitting the woodwork at the cutout ? As Tony says, is it returning under it's spring to it's fully back position ? If it is, then sure, just scoop out a little wood.
Also check stock screws - if they are going in too deep they could be fouling the cocking linkage. Same with the rear trigger guard screws.
In terms of the extra stroke, with stock removed, just take a look and see if there is clearance between the rear of the piston cocking slot and the cocking shoe - at least 1mm needed. Then, when cocking the gun (out of stock), see if you have enough rear slot length to cock it. You may need to lengthen the slot a few mm (dremel is fine) to make up for the extra stroke.
I will say the extra stroke piston makes such a huge difference, so it's well worth it.
HTH - JB
Always looking for any cheap, interesting, knackered "project" guns. Thanks, JB.