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Correct.  That is more of a stutter as if someone was flicking the on-off switch very quickly.  I sense your frustration there.

Is there a dyno close by?  Run it with sniffers in the pipes and watch to see if anything goes out of whack as it runs. Or borrow a data logger and fit an O2 bung and log revs against A:F and look for anomalies. It's hard to read that data on a 2 stroke but might reveal something.

As the anomaly doesn't appear to relate to throttle position, it is more likely to be electrical.

I realize that the two of you have been thorough  and approached this systematically. I'm just trying to look at it with a fresh pair of eyes to see if there's something I might have tried.

Regulator rectifier is unlikely to be the problem, but you could disconnect the whole charging system and run it around the block as a total loss. That would at least eliminate one more variable.

If it is indeed electrical is it possible that there is RF noise from some source that is creating a problem at certain revs/frequencies?  We have a bike on the dyno that hit 6500 and it felt like it was hitting the rev limiter and with that heavy dyno drum driving things it was pretty violent and the deto counter was flashing like a cop car.  The only thing that could have caused it was RF noise from the dyno or the charging system.

The fix was a length of stainless steel braided tube from the hardware store to shield the pickup. That was an Ignitech system with new pickup not an OEM pickup like the RZ, but you could try wrapping the pickup leads in foil just to test it.

With the Zeel software, can you monitor what it's doing?  If so, you might be able to run the bike on the center stand and run it in gear up to say 4k and see if anything stutters or changes in ways that are unexpected. But the symptoms were there with stock ECU, so that's unlikely but you are looking for something unexpected.
 

I can imagine how frustrating this has been for you both.  It's a really odd to have a problem suddenly appear out of nowhere and for it to only impact above 4000 and idle. If it were fuel starvation it should get worse as revs rise.  If it's a broken or shorting lead somewhere it would normally get worse as revs and vibration increase.

We tend to gradually open the throttle so it's hard to isolate rising revs from rising throttle effects. Is there any difference at those problematic revs for example with small throttle openings compared to banging it wide open? with the zeel, it might be an idea to try it with PV closed via software compared to wide open compared to partial throttle. 

Just thinking out loud here but is it possible to see Zeeltronic conditions as it runs say on a dyno or does someone have a datalogger that they would lend to the cause to track mixture, revs, and Throttle position to see if that data sheds light on where to look?

Fuel should not be an issue because if it's bad it usually causes problems all through the rev range.

Another thought: might be an idea to go back to stock carb settings and ignition and PV timing and then swap out the pipes for a different set.  If no change then the pipes are not related though they may exacerbate the issues.

it ran perfect, nothing was changed.tgis was also on a fairly fresh motor. it came on suddenly. therein lies the rub.

Just so I understand it, the bike ran fine after the motor was rebuilt and then suddenly had this mid range issue? Or was it broken in and the problem wasn't identified until it was run harder?

it ran perfect, nothing was changed.tgis was also on a fairly fresh motor. it came on suddenly. therein lies the rub.

Just so I understand it, the bike ran fine after the motor was rebuilt and then suddenly had this mid range issue? Or was it broken in and the problem wasn't identified until it was run harder?

I just read back through the whole thread.  Before I did that I was thinking filler cap not breathing, but I got back to the first page and it looks like the same problem is still there after all sorts of changes.

If that is right, then what changed since it ran right, or maybe it never ran right since it was built. If it ever ran properly then the question is what changed. In either scenario I would start by borrowing a different set of pipes and see if that eliminates the issue.

It does sound like incomplete combustion above idle and below say 4,000 which may be an adverse pipe resonance effect. I don't have any dimensions for the #375 needle jet, so I have nothing to recommend as a possible alternate, but I suspect they are like #284 on late model RD400 which were an air bleed type but with the tall discharge nozzle.

Looking good.  How do you like those bar end mirrors..  I just got a pair of those for the Ducati, but of course it snowed as soon as I fitted them, so no chance to test ride them.

I've got a decade on a 2200mah RC battery. Well I've replaced it three times. But that's not bad.

Excited field, led lights, solid state reg/rectifier. Make sure the carbs are clean and tuned and it's never a problem. Fight to get it started and you're asking for less than excited fields and a broke down bike. 6000mah pack solves that problem for the most part.

You charged that 4cell RC battery with a regular old solid state regulator/rectifier?  How did you balance cells or ensure it was fully charged? I use a 2200 on the GT and a 1300 on the RD but they only run half a mile at a time with say 4 laps a day. with a 1 amp charge rate, they charge for 120 minutes to maintain a full 14.8 volts.

Aircooled 400s in other markets were fitted with the same design of ignition as a Banshee/RZ LC.  IIRC that started with the E model. A few decades back we had E, F and G models in  a few different 250 and 400 formats but for the life of me I cannot remember how the crank was different.

The end had to be larger diameter I would expect - as Mark mentioned and it did have a threaded end to take a nut, in place of the older model bolt.  I wonder if Canadian models retained points or if they were the same as US models.

Mark probably knows the answer to that.

Instead of that battery, have you tried a capacitor (battery eliminator)?  If you need +12v for a relay, that  won't work of course.  I first used a Lucas 2MC capacitor on a 57 pre-unit T100 Triumph with a K2F Magneto and permanent magnet alternator - pretty much the old school version of a Vape from a functionality perspective. That was back in the early 70's and it worked like a charm.

Im currently using the Chinese dyna. I had several real dyna burn up due to leaving the ignition on. Works fine and it was a fraction of the cost.

Funny you should mention that.  I was setting up a custom DYNA for a GT550 triple and three genuine DYNA modules let the blue smoke escape as I was setting the timing.  Not all at one though.  One dies so it was replaced then a different unit died and was replaced. 

Copycat units, no problems and  what appears to be a fatter spark on the tester.

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Has anybody cut off that center cross bar replacing it with a tube? I would guess I would want the tube welded in before cutting it off. I would like to remove it mostly to make it easier to clean from oils as oil get in it as well as the old footpeg mounts and it was a pain to clean....

I have removed that abomination under the motor on a few frames over the years. Weld in a suitable length of tube to replace it and check the spacing for the crankcases.  You could bolt the cases into place and then cut a tube to be a tight fit between the bottom rails

85hp is a significant increase over stock.  Anyone know how those pipes work compared to say SEPC2 early designs? Asking for a friend 

WRT the choke plunger comment.  I have taken to testing them with a vacuum pump (Mityvac or similar) because I have had a number of cases where the rubber tip looked fine but the bike ran rich on one cylinder.  On a TZ I recently had a pair of linked chokes and the linkage was a poofteenth too short and barely cracked the choke open on one side and it ran like a dog until I fixed it.

IS clutch slip common on RZ's?  Mine is 99% stock and I was wondering if I would need new plates in case I take it to the drag strip to get my brain back into gear.

Many years ago, we used to use transistor assisted ignitions.  The idea was that the points would be subject to a much lower load to just switch the transistor and the electronics would carry the load. To be honest, I can't say that any change in performance was noticeable.  Maybe try a relay in the coil power line to get full battery voltage to the coils.  That won't help your points last any longer but should potentially provide a stronger spark.

You could also try a set of Chinese DYna clone ignitions.  I am a fan of Dyna and not of companies copying their IP but you are a long way from here and that might be a suitable solution for you.