Well, it seemed to me that this may be a first time...just by the tension in the words that you posted. I'll try and help. So, in order for me to help, I'll need a bit more information.
What kind of Epoxy Primer did you apply, was it Summit's house Brand?
If it was, how long ago did you apply the Epoxy, is it in the window of re-coating without sanding?
Summit Epoxy Primers can be sanded...if the imperfections that you mentioned are to the point that they will drastically effect the finish, can you sand these imperfections out?
If you can answer these questions, I'll better be able to help you out and hopefully instill some self confidence in you so that you can walk in and hit that Seadoo with a shiny coat of paint.
You'll be fine.