Use IMP as duration for seekers, so up to 5? Although, the book has no restriction on the value of ROF, IMP, or DMG; just Drydock does (and I've changed them for a weapon or two). Change the Evp (Evaporating) trait to affect the DMG value. I don't have Romulan Armada so I don't know how they constructed their plasma torpedoes.
Seeker's actual IMP value for damage purposes is always 1.
Don't change the cost equation. IMO (and I'm not the only one here), seekers are too cheap as is. This might help to alleviate that issue.