Here's my method.
Clean all surfaces that will touch epoxy with acetone and dust-free cloth.
prep the epoxy: Heat an inch of water in an empty margarine container to 85 degrees (I use a stream thermometer), place epoxy containers upright to warm up, wait five minutes (they will equalize at about 80 degrees), and this provides the perfect starting temperature for mixing, bubble evasion, and applying a thin clear finish to penetrate the thread everytime.
I mix the epoxy in an upside-down beer or bottle can. The curved surface works great. Clean with acetone first. Squirt one half of epoxy directly into the other half. I use a small flat laboratory weighing spoon to mix the epoxy - gently - circular or figure 8 motion. Mix 1.5 mins, then let sit for 2 before applying. Make sure the first coat penetrates the thread well (*this is normally easy with Duragloss). I use a quality sable brush with short hair (1/4") to provide a nice firm surface for applying epoxy. Brushes hold a lot of air and air bubbles. I work the epoxy into the brush pretty well before starting to apply to rod. I'll even "sacrifice" some epoxy and spread the initial brush full onto a waste surface. THe first brush full carries a lot of bubbles
For a level finish - try using less stuff at more coats. I prefer a slower motor speed (I think mine is 8 RPM?) because it produces a minimum of centrifugal force on the epoxy, which is self leveling and takes care of itself. You can blow gently on any persistent bubbles to remove them, or use a bodkin