I'm fairly new at rod-building, using LS-2000 Supreme. Having trouble getting the signature area of the rod to come out smooth. Any suggestions on how to get rid of the "wavy" effect?

Apply the finish as even as possible then finish with horizontal (along the axis)strokes. Don't apply much pressure or bubbles will form.

I am convinced the probably the most important thing (well, at least one of the most important things) to learn about finishes is knowing how much to apply in a single session. Too little gets you incomplete coverage, and too much gets you waves.

Lumpyness can be caused by the finish being applied while it is still in a "catalyzing" condition or more simply, while it is very thin. I apply the finish very liberally with the long strokes (rod not turning) before you finish any wraps on the rod then go ahead & finish the wraps. When the wraps are finished I go back to the inscription area and brush off all the excess finish, again with long strokes along the length of the finish areal.
A good way to make a straight line of finish at the end of an inscription is to lightly wet a finely woven cloth with denatured alcohol and stretch the edge along the end of the epoxy-finished area while the rod is turning. This makes a sharp, clean edge to your inscription area.
Tight lines

I could never get LS supreme to level in those areas either & went back to Flexcoat lite