Your friend can probably verify what I was told by an expert on Yamaha pistons, the 403 piston does not have windows and has the same pin height as the HT/LT/DT100.  As you said, the HT/LT/DT100 also used the same rod so my theory of the "redesign" circa 1974 where the clutch arm was moved to the top of the engine is not the answer either.

One thing about the "race" models was that in my observation Yamaha did use different parts more often.  You'll find things like the one-year YZ175 has a different cylinder stud bolt pattern, and head and base gasket unique only to that model, you can't just bolt a YZ175 top end onto 125 cases.   

Best guess at this point is Yamaha used a 2mm longer rod in the MX90?  

P.S.  On the LT - DT100 cylinder swap or it could have been something like the intake manifolds not swapping or something...  or even "cosmetic" like it won't look original.  It was a long time ago.   

 

He's reaching out to a fella in Australia who knows a bit about these. Hopefully something good to report back. Need to get our hands on a 73 MX90 rod.

Probably the intake manifold. I know the LTMX uses a different intake vs the LT enduro.

Stroke is a product of pin placement, not rod length. You should find differences in pin placement on the flywheels and perhaps other changes between the models.

Stroke is the same on the 90 and 100 models discussed.  So there will not be a difference in pin placement in the flywheels.

This brings up an important point.  Yamaha pistons rarely come all the way to TDC, but 2.5mm is a lot.  If the problem is caused by rod length, the piston would also drop down below the ports at BDC.  In my experience, the bottom edge of the transfer ports and exhaust ports line up with the top edge of the piston at BDC on these engines.  

So if the piston is flush with the bottom edges of the ports and doesn't drop below the edge of the ports at BDC, then I'd say this cylinder has excessive deck height.  

If the piston goes down a couple mm below the ports at BDC, then the problem is something like a rod length difference.  

Just something to check.  

Yes, the stroke is the same between the 90 and 100 cc models discussed. However, the stroke is the same on DT1 models from 68 to 73. Within that range, there are different rod length and pin placements on flywheels that will create the exact same situation you’re describing. FYI, the crankshaft flywheels are different on HT1 and LT2. Could this difference for something other than pin placement. Yep, I don’t have them in front of me to examine. But it also could be something to consider to resolve this situation.

Pin placement on crank wheels literally determines stroke.  There is not any difference in crankwheel pin position on a 68 to 73 250 or any engine with the same stroke.  

I cant say anything on the pin placement but i don't think their different. What I can say is we took NOS rods from both the HT and LT and measured them which both are the same length with the HT being just a little thinner. We took the JDM cylinder in question and stuck it on both an HT and LT enduro lower end each with the exact same issue. Piston being 2.5MM shy from reaching the top.
It was brought to my attention yesterday that Noguchi did make a kit for a 90. I cant help but wonder if its actually a Noguchi cylinder. Id have to ask him again about the numbers on the intake side. He lives out of state. Hoping the fella hes talking to in Australia can shed some light on this because im stumped.

Did you check the relationship of the piston to the ports at BDC?

I did not but he may have, ill have to ask him.

Checking at BDC is a better indicator.  

If piston is not a couple mm below the ports at BDC, then the cylinder just has excessive deck height.  Yamaha's generally do...  but not usually 2.5mm.  

If the piston does drop down below the ports, then longer rod would fix it.