Sounds like your fusible link is overloading with driving time and it blows out and shuts your car down. After a while the Fusible link "resets" and you are back on your way until you shut down again right? Are you sure the new Fusible Link is of equal or greater value since you claim to have a new harness. I removed my fusible link from my systems when I upgraded to MSD and a larger alternator. I ran the PowerMaster 120a Single wire straight to the batter with a 6 GA. cable. remove your ballast resistor as that is designed to use a lower voltage coil, not needed with a Blaster coil or MP coil. All those cables from the ballast resistor get fused together I think with a wire nut. I put an inline fuse where the fusible link would be and put on a 25a fuse...then a 35a...then a 40a...thats with everything on....the heater, the stereo system, the headlights, the everything..I ended up replacing the 40a fuse with a 40a reset breaker from a 737 cockpit (my friend worked at SAGE Air...) big red button on the firewall...looked clean...people never knew what it was. Never blew another fusible link.

One other thing to check is the Starter relay...it supplies your cabin with all the necessary power...if it heats up from a bad ground or a leak in the circuitry...you will blow the fusible as well..

And finally, the only other time my Charger has slow blown a fuse was when the wiring for the power seat ended up getting grounded to the floorpan because the shielding came off the cable..I was driving to Vegas at 3am...stopped for gas 3 hours out...and she wouldn't let me leave the gas station until I dragged her to an electrical shop by tow truck and he found the broken wire under the carpet.