Fish eyes are annoying and are usually caused by contamination. When I make mine I have plastic garden "closhes" that I place over the rod to protect it from dust, and particularly sprays such as furniture polish etc. They get put in place if I have a break from the whipping as well, just in case.
I also wash my hands several times during the whipping process...just in case.
They can be fixed if you notice them on the drier. Take a clean needle (I wash in acetone first) and just "scribble" around the effected area, moving the epoxy about and drawing it into the centre of the fisheye. If you notice after the epoxy has set, you can either clean really well with acetone/a rod cleaner and recoat, or, if you have a bit of a rugby ball going on, take some wet and dry and sand the epoxy back a bit, clean and then recoat.
As for he rugby balls...we have all been there
If I am in a rush I tend to end up with them as well, or if the epoxy is going off it does not level well. If I am doing for someone else, I tend to put 3-5 very thin coats on (I thin the epoxy slightly too) rather than a base then top coat. You get a lovely finish, but it take ages.
Having said all that, you have a rod you have built, don't worry about the looks too much, just get out there and enjoy!