The problem started with the pickup and stator. Strictly from a cause and effect perspective the last thing you did before the trouble showed up is often the cause.
Is it possible the pickup has come loose throwing the timing a bit off? Is it possible to put the pickup in upsidedown or backwards?
I would also check the throttle position sensor on the carbs, that is the signal the ECM uses to advance the spark, so if its failed, not adjusted right, or the connector is loose, the ignition timing would also be off. That is a really easy thing to check with a volt meter just twisting the throttle.
From the top of my head Im not sure if a backfire at constant RPM is from running rich or lean - what do the spark plugs look like? The idle, PMscrew ports, and the main jets are sequential. The main jets do not even open until the throttle is near half way open, so if something is only bad at highway speeds, it points to either the main jets, or maybe the PMscrews being a bit off which makes it worse when the main jets engage.
Since you had the carbs off also make sure the choke (enrichment) is working correctly and not staying on when you push the knob in.
One other thing: if your air filter is not white like paper it needs to be replaced. My 650 started running weak at highway speeds when the odo got to 25k miles, the air filter looked grey like a nasty old teeshirt. Replaced it and the bike came back to life. That whole thing in the owners manual about blowing it off with compressed air is bullKwrap.
The other question is whether the valve clearance has been checked or adjusted recently? If the valves are getting tight they will not close all the way, and backfire. Unfortunately you need to pull the carbs loose (enough to get them out of the way) to check the intake valves.
I know this is a lot of things to check, but a lot of things can make an engine backfire.
Last edited by KCW; 06-11-2019 at 10:29 AM.