I am currently doing a head stack replacement on a Samsung 500GB 3.5" HDD and having problems removing the head stack as the head stack will not come off the spindle.

Please advise.

This is no surprise. The Head Stack has a limiter in the magnet keepers that forbids it come off the spindle and platters.
Remove the upper part of the magnet first.
OR
Risk to remove the platters first.
But I say theres a 90% possibility of damaging the drive in second method. Send it to the service centre is my advice.