well to start with what you currently have is much better than an ender 3.
You already have a direct drive extruder, dual z-axis motors and side support rails with dearings on the printbed. You Lose all of those and the speed and stabiity they bring with an ender3.

Also you already have a much better setup for printing flexibles than you get with ANY current creality printer.
For flexibles you need direct drive - yes you can do it with a bowden, but you end up printing really really slow and retractions never really work properly.

The screen and board are a good idea. I'd personally go with repetier over marlin for the firmware - but that's just personal choice.

Not sure why you want to change the hotend.
I wouldn't bother (well I haven't).
As far as changing filament goes - that will come with the new firmware.

As far as the frame goes - all that need is fixing to a solid base. I used a sheet of 4mm aluminium, made some brackets and feet and bolted tha whole frame to it.
As far as bed levelling goes. Change the current nuts to nylon locking nuts and screw them all down until the springs are reallly tight.
Adjust the z-axis endstop for the new height and level. That will stay level (particularly if you've bolted the frame to something flat and solid) almost indefinitely.
All an autolevel sensor does is adjust for a non-flat bed. You still need to do the manual actual level.

So stick with what you have and do LESS to it.

Board and screen.
Stable base
change the bed nuts to nylock
Job done :-)

Autowiz on the other hand would have you totally rebuild the entire thing - I like to think I only change what NEEDS changing. He just likes building stuff :-)