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Did you check that the choke plunger is sealing ok?

I have tried to block it, but seems difficult and I am not sure that I actually had it completely blocked. Any suggestions on how to make sure it is blocked? I just stuffed some thin plastic under the plunger. I think it was blocked, but not for sure. And wouldn't the right get the same extra fuel as the left if it were leaking? I have ran it extensively both with and without the cross over. No difference.

There are probably others ways to do it, but I use a MityVac or copy with hose and a tapered tip which is inserted into the outlet on the motor side of the carb.  Apply vacuum and see if it holds it.  It's a bit of a PIA to keep the tapered tip in place and not leak, but patience pays off.

The short answer to the original question is to remove the foam and clean up the base.  Then cover it with a layer of reasonably thick plastic or apply a generous coating or two of mold release and lay s couple or three layers of fiberglass and resin on top. When it has cured, remove what is not the new seat base and trim it to size.  get a piece of foam cut to match the seat pan and take it to an auto upholstery place to get the cover of your own design made and stuck or stapled to it.

Attach velco to the seat base and seat pan to hold them together.  Done.

The small one is easy, but for the large one, see the blocks on one side?  They position the seal the correct distance from the outer bearing race, so it's easy to work out which way is in and which is out.

If it runs better with the old bent needle than it did with a nice shiny new needle, which seems to defy logic - Unless there is a matching problem with the corresponding needle jet. Ebay Australia has a Keyster replacement and CSMNL look like they have stock ones.

Might be worth popping them both out and checking the orifice to see if there are signs of gouging or interference on the bad side. If the bent needle has created a larger that spec needle jet orifice, that would create a rich fuel situation causing it to bog down.

My machinist is not in the very interested in machining a thin wall tapered tube unless I can guarantee that I have accurately measured the tapers to be sure it will work. It might be simpler in my case to buy a suitable VAPE combination of parts or to have the crank nose built up with weld and machined to the new larger size - assuming that is possible given the size it has to grow to.

I may have to take a stock alternator rotor and pull the bub out.  That would give me an ID that matches the shaft diameter and taper, and have the OEM alternator rotor machined down to match the new rotor.

Thanks for you input

OK.  I thought that is was dying out like a flat battery or fuel, but that sounds more like a pipe effect.  At a steady say 35mph in 5th or 6th, just curing along, if I open the throttle all I get is intake noise as it slows down.  Drop a gear or three to get the revs up and it sings, but at lower revs, no amount ( little or large) of throttle makes much difference, except to intake noise.

I have an older pair of Spec2 pipes on mine and as long as revs are high enough, it is very responsive.

if you could borrow a different set op pipes to do a back to back comparison, that might shed light on things.

Were you able to run it with the 3d printed taper adapter or did you use that as a model to get one machined? The reason I ask is that I want to use a modern inside out rotor with side cover mounted stator on a GT750 and I would need a similar, but larger adapter.

While you are loading up the parts cannon, I wasn't sure if it dies suddenly like hitting the kill switch or it just sort of dies away like running out of fuel. The first suggests an electrical issue and the latter, fueling. And IIRC, there was an issue at part throttle/low to mid revs that clear up at higher revs.  That would suggest PV timing, pipe resonance or needle portion of the fuel map. If it feels more like it is tightening up and then frees up it could be too much advance at those revs.

Just thinking out loud again, which is always dangerous. 

I have a blue dot caliper here somewhere that I bought for our RD350 drag bike.  I used an alloy repo caliper with alloy pistons instead.

I did measure them to compare with higher quality calipers.
They were really close to each other at the tip, midway and near the top, plus overall length.

That still doesn't explain why I'm running the highway or interstate in the good rpm range and it slowly winds down to a crawl or completely stops

If it does come to a stop, it will kick back to life like nothing happened. This behavior started the bowls-running-dry theory that has been disproven and appears electrical in nature.

That particular symptom sounds exactly like a partially blocked air vent in the filler cap. Bowls run dry and when the bike stops, enough air gets in to allow fuel to flow. 

Going back to the first post in May, one needle was replaced and the tank was sealed.  Did either of you check the needle dimensions and compare those to stock or the the needle that wasn't changed (or the one that was)?

We may have covered this a few pages back, but have you tried swapping a different set of pipes - just to see if the problem goes away?  If you were closer, I would offer my RZ350 as a test mule for swapping parts. IS there anyone closer with an RZ that you can borrow parts off to do back to back testing of swapped parts?

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.