RT325, Manual doesn't state checking with the resistance cap on or off, I checked with it on to get my result. Sorry, but I'm not sure what you mean by getting a positive result on the black wire between points open and closed. We set the points with a points buzz box.

I got the bike running again this afternoon. Flywheel off, originally cleaned the new points with emery cloth, since then, I've now run a business card through them, they should be good and clean. There was some oil laying in below the flywheel, I cleaned all that up, not sure where it came from as the new seal we'd replaced on the left side crank is nice and dry, anyways it's all clean now. I sprayed the solder joints on the condenser with Brake Clean just to make sure none of the oil had contaminated them. Checked continuity from where the coil connects to the the main wire harness then out again to where the connection is to go down to the points; good, then from where that connection is down through to the stator to the points; good. Reinstalled the questionable coil and hooked it back up, the ground is nice and clean and the black wire/bullet connector is fitting as it should. The previous owner had installed a different plug cap and it's still in place. The current owner of the bike was running a resistor plug, I got it to spark (and that's what he was running Saturday when it quit on him) but found an old, correct, non resistor NGK plug, cleaned it and used it; nice strong blue spark. I swear the first few kicks there was still no spark, and then there was spark! Put the tank back on then up and down the street in front of the house and all seems okay. We'll see if it'll keeps running once the engine gets good and hot; 45 degrees out today with a light rain, a ride will not happen today.

Congratulations!

Something I was expecting someone to mention is that it sounds like you used "kit jets" in the carb from what you said in your first post. 

Bad idea, even if they are stamped with the same size, that's meaningless unless the jets and slide needle have the Mikuni "square in the corner of a square" trademark symbol stamped in them.  And I've never seen a Yamaha carb kit that came with Mikuni jets.  Companies like Keyster use their own "proprietary" calibration sizing but generally stamp the Mikuni numbers on the jets.  

Many people have had issues when running "kit" jets in these old two strokes including things like fouling plugs, not wanting to restart when hot, or poor running in general.  

Original Mikuni jets and slide needles are readily available in most cases.

Ahh, Tore the carb completely apart shortly after the young man brought the bike home and cleaned it in my ultrasonic cleaner. Replaced the gaskets and o-rings and the only hard parts were the needle and seat for the floats. All the other pieces were in good shape and cleaned up well.

Not sure what I said but would've meant getting a definite variation on an anologue meter between open & closed.  My meter is faulty & can't zero it but I know when it moves its showing points contacting & seperating. I think Mark T says should be zero when closed--because it's all going to earth. Then very little when open as I guess you're then seeing the resistance of the primary source coil. If nothing changes at all from open to closed then need to look hard in the points area. I know people say points must be clean & all that but he'll if you saw mine which never falters--its strange what works at times. But they sure must contact. Could lift points out & disconnected to check if there's something off the planet going on as should show a definite result. I can see I would've said positive result just thinking back but just meant to get a definite result that's all.