When I came out of church and got on my bike the battery was completely dead not even lighting up the neutral light. Since I had planned to ride to the beach with my wife I decided to jump it off her bike and contiune the trip as planned.After several hours of riding and several jumps(the battery did not charge a lick while riding) the bike started to sputter and misfire as if the timeing suddenly went haywire. I pulled over and the bike was still running but it was running rough and it stalled out when I tried to pull off. I had just fueled up about 50 miles ago so I had plenty of fuel.At first I thought the charging system was malfunctioning because the battery never took a charge, but after I got the bike home I took the battery off and noticed the ground cable was not very tight. Still the battery did not cause the bike to misfire and what ever happened happened all of a sudden.Reading the honda manual I saw that the ignition control module can throw off the timeing. Having never worked on a bike I was hoping someone could point me in the right direction. By the way the bike is a 2000 Honda Shadow Spirit.
Thank You,
Joseph

Based on your description, I see two unrelated issues:

1. Loose cable implies charging system damage. Regulator or alernator diode damage. Possible battery damage. Been there, done that when I had my car painted and they didn't tighten the battery cable.

2. I doubt it's a timing issue. Bet you got gas with water in it.
Seafoam carb cleaner added to the tank in the proper proportions should fix that.

3. The bad cable could have damaged the ICM too, but I'd rule out the first two items first.