How close should the nozzle be to the substrate? I have my nozzle close to the substrate that I am printing on, so that a piece of paper can just about slide underneath it freely, without catching. Is this the right way to do it?

Traditionally, using a piece of paper (about 0.004" thick) gets you close to your appropriate standoff. However, if you adjust your layer thickness, your standoff should reflect this. Ideally, you will set your standoff **roughly** with a piece of paper or other type of shim stock, then "fine-tune" the standoff during a benchmark print.

If I'm remembering correctly, the ideal standoff is 1/2 to 2/3 your desired layer height.