How far above the printer bed should the extruder nozzle be while printing or for "Z" home?
Answer: about a little higher than the thickness of a sheet of paper. You want it down as far as it can go without actually dragging on the surface. In some instances this will not be possibly, however the idea is that the x/y does not loose position while z axis is at zero and x/y moves. Keep in mind the first layer will raise the z height before print.
What causes occasional blobs while printing (using PLA, 0.35 nozzle, calibrated extruder)
Answer. This is hard to pinpoint because several things cause it. What happens is for various reasons the area that is being printed is double or triple dosed with the filament from the hot end. Either a stutter, a lack of motion in x/y, or a slow change in z height, or lack of proper flow, or z height change. There are several reasons. You will want to start by watching the motion of your machine when it happens.
As for your extruder. Never believe the extruder temp. It is +/- 5 deg c! If set correctly. Just set it where the feedstock flows and works at the speed you want to print at reliably. On the high end of temp range you need to worry about pla crystallizing, on the low end you need to worry that it does not melt fast enough to push thru extruder. Likely now your hobbled bolt is filled with plastic and no longer effective. Take a nail and place bolt under hot water, and peel the plastic out of the teeth. I would recommend also turning motor current down further on e axis to have it stall out so you don’t strip feedstock. If motor stalls a lot then raise temp to make it easier to push feedstock thru.
hope it helps, hopefully many others will reply and aid in to help you with your issues.....