Drained Battery, Misfiring, Blown Fuse Mystery

[photojourno]

After driving 60 miles a day for a week, my 1980 cb750k died on me. I lost power and stalled out. When I tried to restart the bike it wouldn't turn over and eventually the battery died. At this point, at 4000 rpms, my battery output was 11.88v.

I started poking around and found a melted pin in the wire harnesses joining the rectifier-regulator to the stator. I replaced both of those items. I also came across a deal on ignition new coils so i replaced those too just for good measure.

Now at 4000rpms, Im reading 13.6v. The pins in the alternator are holding up just fine and the rotor tests out good but its not the 14.4v I was getting when I first got the bike a month ago.

AND

Now my bike rarely starts. When it does it misfires. It won't stay on at idle.

There is no draw on the battery when the key is off, but when its on, the battery drains after 6 or 7 attempts to start the bike. My headlight fuse blew when I tried to start it this morning. I took the headlight fuse out and tried to start the bike, then the next fuse over blew. The bike on the center stand, and when I do get it running, the back tire spins even though the neutral light is on.

A few questions: When I installed the coils, the black wire goes to the negative on each coil correct? Is misfiring a dirty carb problem? Could it be a clogged jet or stuck float thats causing the battery to drain? Would a dirty carb account for the lost volt when the alternator gets up to 4000rpm?    

Any help would be greatly appreciated.

[TOOLS1]

The carbs and electrics have nothing to do with each other, so they are not affecting each other. The fuses blowing are an indication of a dead short, or drawing too much amperage for the circuit. It seems like from what you describe that the starter is drawing from the other circuits somehow. Maybe start checking the grounds. Especially the ground cable.
13.4 volts at 2500+ RPM is good. On the coil wires, the black should be "hot" to the coil, and be connected to the "+" terminal.
The popping, backfireing, and not idling are most likely caused by a vacuum leak. The intake boots are known to leak if the carbs have been removed and put back on.
TOOLS

[photojourno]

Thanks Tools. Ill check that stuff out tonight. At 2500rpms Im reading 12.6 volts.

[shinyribs]

I was scratching my head on the fuse issues, but I really think Tools is on to something there. Makes perfect sense.

The back tire spinning while idling in neutral is normal. These wet clutches just do that. No worries there.

The poor running could just be due to a weak battery. These engine's Ignition systems rely heavily on a strong battery. Since it seems your running issues came about instantly after the electrical issues, that may be all it is. Seriously, they will run awful with just a weak battery. Good luck bud.

[photojourno]

Thanks. I just changed the battery, fresh off of the charger it reads 13.5. Ok just to double check, the black and white wire going into my ignition coil goes to the positive terminal on the coil?

[photojourno]

The ignition coil wires are all different colors on both sides. I think they were replaced. If the coils are wired wrong, that would probably also account for the misfires right?