If it worked fine before you stripped the nozzle down it's likely to be something you did during the process. Changing a load of electrical variables is probably going to take you further from the resolution. What you did was mechanical so I'd be looking there rather than an electrical adjustment.
Have you got an adjustable feed tension spring? Did you remove it during the strip down? If so, it may be out of adjustment and affect the flow rate.
Did you clean the nozzle? Did you use the correct size of drill? When tightening it all up, maybe you've deformed the inner PTFE tube, constricting the flow?
Just a few thoughts.
In fault finding, I've always worked on the premise that if you've changed/adjusted something and it gave a worse result, that's the first place to look. Try to undo what you just did to get back to your original state. If it worked with a certain motor voltage/installed firmware version before you stripped the nozzle, it shouldn't need them changed to work again.
Anyway... My two cents.
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Soadyheid.