Puller?
First thing you need to do is make sure that you indeed have the correct puller??? Even though you did get the whole clutch off with it previously, just check to make sure, so you dont end up damaging the clutch with the wrong puller. The reason I say this is because when using the correct puller, the operating half of the clutch should stay with the fixed half until the whole thing pops off. The correct puller actually pulls the fixed half off the crank, and should not contact the threads on the operating half durring this process. After the whole clutch has been removed you then smack the head of the puller with a hammer to split the two halves. I am sure you already know that, but just want to be clear on this.
Now getting a stubborn clutch off is a real pain, but keep your cool. I have had the best results with the grease by putting a glob on the end of the puller. When that does not work I put the end of the grease gun inside the bolt hole of the clutch and filled'er up(messy), then put the puller in and giver a go. Next to last resort is the impact (1/2" impact not 3/8 drive) and it should pop. If you still cant get it to go, I then have heated the shaft on the clutch with a torch, and hit it with a impact. when using heat, do only enogh to get it off, as the seal on the pto main bearing is danger close.
I am not a big fan of smacking the puller with a hammer while its on the machine, as you are in effect driving the crank through the block, and can result in what they call crank walk which can destroy the bottom end of a motor. This is also why the impact should be used as the last resort as well. It may be safer than a 2lb hammer but not much.