Good questions. The stones aren't hitting all the way to the heel of the blade because of the choil; this is really common with Spyderco knives. At the moment, the only solutions are to either trim the plastic from one side of your stone handles or use the thicker waterstones. Another possible option is to remove the stones from their handles, add a spacer piece and then mount the stones to the spacer for extra height.

For the tip, I'd recommend mounting the knife more centered in the clamp with the tip closer to the vise. You can use this guide: Finding the Sweet Spot to help find the right position. It also helps not to over-rotate the stones on the rod as you approach the tip. If you imagine keeping the stone in the same plane throughout the stroke and adding just a tiny bit of pressure with your thumbs, you'll be able to get the tip needle sharp.

No matter how hard I try, I can never get a blade dead center according to the angle cube. I'm always at least 3/4 of a degree off, most of the time more.

So I ask, how much is too much? How much is acceptable?

Thanks guys.

Just for the record, the left side of the blade always seems to have a slightly lower angle than the right. It's been that way on every single knife I've done, despite me making sure it's within 1 degree of being centered using an angle cube.