ok, i think that you're trying to do a life extension program for a P3. you know something of fatigue, but i sense not much formal training or experience; forgive me if i'm wrong in this.
this is something that is Way to big to solve in a forum discussion.
if the palne has consistently been flying at a lower AUWt than Lockheed's assumed mission, then there is something to be gained for Most of the structure. the landing gear probably won't change. the fuselage probably won't gain much either, dominated by pressurisation.
Some military planes fly with known cracks, but only after Alot of analysis. They need to prove that the crack will still hold ultimate strength untill the next inspection.
Get some formal training in ASIP, DTA, fatigue, etc. Get some experienced engineers to work through the problem with you. talk to Lockheed. this is a big project, several manyears of effort.