Offshoreonly.com - Msd Ignition Troubleshooting

I Have Run An Msd Marine Set-up For Approximately 100 Hours With A Good Service History. Last Wednesday I Went To Run The Boat And Neither Engine Would Start. First Step Was To Check In The Caps For Corrosion Which Was Present ( This Happens About Every 6 Months). I Returned With New Caps And Replaced Them. Unfortunately, When The Battery Switches Were Turned On The Msd Box On The Port Motor Actually Smoked Out. I Immediately Turned Off The Battery Switches And The Smoke Stopped; However, Both Msd Boxes Were Now Toast. I Replaced All The Batteries In The Boat After A Voltage Test Showed One Of The Batteries To Be Low. Replaced The Boxes With The Correct Marine 6m2. Both Engines Now Run. Now The Problem Begins. The Port Motor, Which Is The Motor That Had The Msd Box That Smoked Out, Now Runs But The Timing Moves Iradically When The Engine Is Under Load. I Can Put The Correct Timing In The System At The Dock, But Once The Boat Is Taken Out And Put Under Load The Timing Jumps All Over The Place. The Engine Then Backfires Through The Carb At 2000rpm Which Is Consistant With The Timing Issues. I Have Now Changed To A New 8562 Distributor Because Of Corrosion In The Old Unit, New Plug Wires, New Plugs, Run The Engine With The Soft Touch Disconnected, Changed Fuel Filters. I Have Consulted Others That Have Said The Low Voltage Could Have Caused A Reverse Polarity Condition In The Inginition System And Started The "smoke-out". I Have Not Changed The Coil, But The Coil Does Fire And The Enigine Only Has The Lean Misfire Under A Load. Could A Coil Still Have A Reverse Polarity Situation? And Cause The Problem? What Other Items Can I Check? I Have Also Switched Msd Boxes And The Same Condition Existed On The Port Motor. I Also Swapped Carbs And The Same Condition Existed On The Port Motor. I Have Isolated Batteries To The Port Motor And The Same Condition Remained. Any Points To Look For In The Harness? Any And All Direction Will Be Greatly Appreciated. I Need Help. Thanks