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Organicjedi, you have described my situation with my RD400 almost exactly.  I have Dyna S pickups.  Bike goes like a missile until it mysteriously will stop sparking on one cylinder. I had a set of the Economy coils on it, so I went back to stock.  Ran great, then suddenly after many miles, it is back to a one cylinder RD.  Limp home. Sucks.  Wait awhile, wind changes direction, and suddenly it is a missile again.  I have eliminated the coils, 7mm wires and spark plug boots.  Only thing left is the Dyna  S pickups. 
Will look for set from ebay or wrecking yard to start swapping them out. Will update when I solve the problem.

Longer stroke = more oil.  That is what I thought.  Last night I remeasured the gap.  Part of my problem is how I was using the feeler gage.  I would slide the gauge up the round ramp to enter the gap.  This ramp and gap was well greased and would eaisly accommodate a up to an extra .003 of gauge.  Difficult to get a feel for resistance.  So, last night, I cleaned the round ramp and the contact washer with brake clean. I put back the OEM combo of shims. This time instead of sliding the gauge in from the ramp, I approached the gap from the side, on the radius.  No influence of grease.  The measurements I got this way were agout .012-.013.  Yamaha in their wisdom used 3 shims, one of which was about .0025.  I suspect this was done to provide easy one time adjustment on a well broken in pump. Mine has about 21,000 miles on it.  After pulling the .0025 shim out, I am now about .0095 gap.   Looks good. Added back a smidge of grease. Test ride today!

Update.

I using the 6th gear to turn sparkplugless engine work fine. The gap read about .018. I always have brass shimstock on hand, so I built a shim and now have about .010 gap.  That service manual  says .008-.010.

I have never dismantled a oil pump, so the function is a bit of a mystery to me. 

Question 1. comparing .008 to .010, which one injects more oil, smaller or bigger gap.

I've taken the RD400 for a couple of rides now.  I am using the latest Klotz synthetic TC-W3 oil. I am shocked at how smokeless the RD is. Almost scary. 

How much of this smokelessness is attributable to the Klotz, and how much to shrinking the shim gap from .018 to .010?

Awe, nice to have knowledge like this to lean on!  Thanks.

I'm real close to starting my RD400 up after restoration. Adjusting the oil pump cable at wide-open was easy, but I am confused about the pump stroke adjustment. I have the RD400C service manual from this site, pictures are grainy.  The instructions talk about rotating a plastic starter plate and using a feeler gauage set.  My pump is a 1A0, and there is not a plastic starter plate.  It looks more like a pump from a mid 80s RZ.  Does anyone have instructions on how to adjust the 1A0 pump stroke.
Cheers!