try a remote tank just to eliminate fuel supply as an issue. Take a volt meter with you, when it shuts down, check voltage at the + terminal on teh coil, it should be above 8 volts, if it won't start back up, run a jumper wire from the + terminal on teh coil to the + termoinal on teh bagttery, if it runs then, you're resistor wire(purple/white stripe) is breaking down. Cut the harness back till you can find a purple wire, splice a new purple wire intoit and repalce the purple/white with the new wire to the coil. Also, make sure the wires to the pertronix didn't get chafed when you installed it, make sure the black wires runs to the - terminal on the coil is good and secure. Is that a new coil? Two more things, disconect the tach wire at the coil(grey)and see if it runs better. If that doesn't help, disconect teh shift assist wire at the shift switch(white/green stripe). Becarefull if you disconect the shift switch, it will be difficult to get it to come out of gear. You may have to cut teh switch off to get it to shift. Stay out in open water doing this test(away from docks and other boats)
If that doens't get the job done or if youhave any questions, call me next time your on the boat, I'll walk you thru a few things. David Hall (843) 532-9148