no need to remove the board completely,just discoonect the 3 ribbons and then turn it over to expose the underneath,best is lay it beside the drive chassis.
as far as i know,it wont matter what way round it gos.
as for dosflash32 or jungleflasher,just try either and see which one works for you ie:which picks up the drive and allows you to read it.
the cut traces need reconnecting,how you do it is up to you,solder bridge,wire or conductive paint,its up to you.

I didn't disconnect any of the ribbons. Once the screws are gone you can flip the board without removing them.