So your gun may exhibit better than average accuracy. That's great, but the fact remains that even after going back to Ruger and having nearly all of the fire control group parts changed, the gun still exhibits the doubling issue.
That would yield one of three possible scenarios.
1) Something that was not changed out is still out of spec.
2) Something that was changed was swapped with another out of spec part.
3) There is a fundamental design problem with the action of the SR45, allowing a completely in spec gun to double.
I will discount #2 because the difference in time between when you gun was manufactured and when it was sent back should have in all likelyhood resulted in a different lot of parts being used as a replacement. Additionally I would expect that if it were related to a particular lot of parts, Ruger would have seen this issue in other customers firearms, identified it, and recalled those guns.
#3 can be discounted because if it were a design issue, there would have already been a recall, as lots and lots of people would have been seeing this behavior.
This only leaves #1
Regardless of whether or not it does it on every single load, just the hot ones, just the middle ones, just the light ones, with one particular shooter, or only on the 3rd Saturday of every other month when the moon is full, the gun is not functioning properly with factory spec parts. We are not talking about a FTF or FTE type issue but a gross failure of the trigger mechanism as a whole, allowing 2 rounds to fire from a single pull of the trigger.
Your modification of the factory parts is not the answer to what is going on. Even if you get the behavior to stop, which it appears that you have, the root cause still exists and could easily come back if your modified parts are changed out. The design of the gun is such that given all of the tolerances in the manufacturing process, and even considering tolerance stacking, the gun should still function as expected. Yours clearly does not.
From a legal perspective, you have liability as well. You have a firearm that you know will fire 2 rounds from a single pull of the trigger (this is not bump firing, this is considered fully automatic fire). The only course of action that is considered legal, from a BATFE perspective, is to have that firearm sent back to the manufacturer or to a licensed gunsmith for repair. Each and every time you take this gun out to "test" your latest modification, you are in direct violation of the law, if the gun doubles. You can say that this is just fantasy or something that would never actually happen, however the BATFE did obtain a conviction for exactly this scenario (United States vs. Olofson, 2009)
Ultimately, it is your gun, and you are more than welcome to do with it what you wish.