Electrical Mystery

[Yamahammer1200]

Engine starts and runs great.  On occasion, it will freak out.  It happens when I slow down from highway speed or higher revs.  The tach will drop to zero and I lose some, but not all power. If I rev the engine, it will eventually snap back into shape, and I can get home as if nothing happened.  I have  a new Shorai battery that reads good. 
This same issue happened with the old battery.
I have checked the ground wires from the battery and they are good.
Am I just looking for a loose connection somewhere?

[Pat Conlon]

Sounds like your ignition is cutting out....the loss of the tach signal is key.

The tach signal comes from your right side coil (grey wire) the coil that fires #2 and 3. It sounds like if you are losing power without the entire engine shutting off, you could be losing power to that right coil, with the other coil (left side coil#1&4) keeping things alive until the right coil wakes up.
So check the connections to your right coil.

If the entire system is shutting off (both coils) 2 common areas to check:

1) The sidestand switch: a normally closed switch (meaning closed when in the run position, sidestand up)
    Check the continuity, although it may not tell the whole story. These switches can be cunning and baffling. Fine when you test them only then to act up on the road.
 Isolate the switch to see if the symptoms goes away. Follow the wires from the switch up to under the side cover. Locate the plug. Disconnect the plug and on the male plug (engine side) make a jumper wire with 2 small spade connectors, connect them to the male prongs and close the circuit.
Go for a ride. See if the problem goes away. This is easily reversible with no cut wires to deal with.
******Don't forget to retract the sidestand******** Don't ask how I know this.

2) The run/stop switch on the throttle side of your handle bars. This is a poor design on this switch. You need to disassemble and clean the contacts. You can bypass this switch but it involves cutting wires, not recommended.

Hope this helps.

[Yamahammer1200]

Thanks for pointing me in the right direction. Thank you Mr. Conlon.
I will investigate while I install a relay harness to the coils.
The horn relay install was successful...I started with the easy one first.
Now the horn sounds like a very large roadrunner!