TOPIC:

When you got your bike home and your coils read around 8V what did your battery read?
I'm wondering if your charging system is suffering below WOT.
The running great for 200 miles then shit could be a slowly draining battery.
Then the hit to WOT gives the battery a boost for a little bit.. bringing 2&3 back online for a little bit.

think F64 is on to something. Are you driving with highbeam on for extended periods? Recently went through something similar with a friends bike. Loose wire in the handle bar switches was grounding out and causing the battery to slowly drain over many miles of running until it would die. You may have a extra draw somewhere.

F64, I wish I had thought to test the battery voltage.   {face palm}
I do not ride with the highbeam on, but I have noticed the headlight will switch to hi-beam/flicker in the garage if I barley push up on the low/hi beam switch.  I will go into the RH switch and wiggle some wires around then re-solder the connections.

I do have an agm battery w/ a mosfet reg/rec.

If you are using the latch connector to splice the Dyna into the loom, there could be intermittent resistance. I had this problem.
Also the Dyna S has a long dwell time and may be depleting your battery if you have a 2 phase charging system & run 3ohm coils.
The dyna works better with 3 phase charging. Alternatively 5 ohm coils for a 2 phase system. 
Copper plugs worked better than Iridium from my experience. No resistor plugs and caps.

 

I second the point about the latch connector.  Toss it out.  There should be a spare hot wire near your headlight.  Use that to power your coils.

I didn't want to chance that crappy splice, so I soldered in the connection.

I'm using a Mosfet FH020AA I'm pretty sure it's a 3 phase. 

Put a meter on the battery posts(metal part of battery) not the terminals.
Check voltage at idle with and without high beam
And 4000 rpm
With and without high beam.

I think I agree here it’s in the electronic circuit. I don’t ever recall anyone have a fuel deliver problem come and go after an extended ride. Not ruling out a vent or heat related issue but Typically a fuel issue will present within the first mile or so. Besides fuel on these is strictly mechanical they either work correctly or don’t, not the kind of system that works intermittently. I pulled the tank on mine recently, shortly after a nice long ride and was amazed at the heat buildup under the tank. Everything, frame, coils, brackets were almost to the point of too hot to touch. No wonder we have coils the go bad. I never realize it would be that hot. I’d quickly investigate the tank vent, and potential heat/vapor issues to rule those out and start digging into the electronics. 

Have you had a chance to check more voltages? My '78 Z1-R is doing this same thing. Usually on start up, running 2 cyl., then on 4 after a few seconds, then runs fine the rest of the day. It has dropped 2 cyl. after running, but it's usually only at first start up. It has gotten progressively worse lately, and eventually it won't run all 4 cyl. consistently now.
 So, I did the WG relay mod last night because I was getting between 8.5-9.2V at the 1-4 coil terminal, with 12.5 at battery. Even after that the bike is still doing the 2 hole boogie. THEN,  I thought I found the culprit when I found a loose wire in the crimp connector at the coil terminal. I was ecstatic, thinking F yeah!!! Wasn't it. I was able to get it to run strong with a jumper wire straight from the positive battery post to the coil post on 1-4 coil is the reason I thought it had to be that connector being the problem, but now it's back to 2 cylinders again. Scratching my head over here. 
 Is your Dyna S kit new? Is it the later style without the box? Where are you grounding your ignition circuit, and your relay?

I had the problem of a coil intermittently dropping in and out with the Dyna S. The cause was the feed  terminal. I had been tinning the wires before crimping and shrink-wrapping. The flux from the solder must have created some resistance. I read that the correct way is either crimp without tinning or crimp and then solder. I've had no problems since changing the technique.

BlackZ1R
Fire up the bike.
Meter on DC V
Black probe on negative battery post(metal part of battery.
Red probe on the 1,4 coil positive post(metal terminal on coil not the connector) .
Note voltages firing vs not firing


Move the red probe to the negative post of the coil.
Note voltage when firing vs not firing

wrote:

I had the problem of a coil intermittently dropping in and out with the Dyna S. The cause was the feed  terminal. I had been tinning the wires before crimping and shrink-wrapping. The flux from the solder must have created some resistance. I read that the correct way is either crimp without tinning or crimp and then solder. I've had no problems since changing the technique.

Haha, are you sure you didn't wire my bike too? Weird that I found the same thing on the 1-4 coil wire. The end was tinned then crimped. The crimp didn't "bite" into the wire, so it was pushing in and out of the ring terminal. I cut it off and crimped a new terminal on, then soldered it. Running great now.
The best thing I did was change the battery out. I noticed it was dragging slightly after it got up to temp. I pulled the battery out of my KLR and swapped them out. KLR battery is much stronger, everything working much better on the Z1-R now. Z1-R battery has no problems cranking the KLR... so far.