I also tried to craft a phaser omni with pen, but I eventually read in the comments in a youtube video that players wished they could craft omnis with unique modifiers. So I was forced to realize it was impossible to craft omnis with unique modifiers.
I am also having the exact same problems with my deflector and shields not having the right hit points as they should, my turning radius most likely is not right either. These problems are also being discussed on reddit. Please fix this!