It is difficult to tell since it is a translucent filament, but in your attached photo it sort of looks like your first layer may be getting too squished. What version of Cura are you using? If you are on one of our later versions of Cura (anything labeled as Cura Lulzbot Edition) when you flashed the firmware it would have overwritten the Z-Offset which controls the distance between the nozzle and the bed during the first layer of the print. If you are on a newer version of Cura and haven’t yet restored your Z-Offset to the correct value for your printer we can help you figure out what that should be set to by using the serial number for your printer and help walk you through that process. If you would prefer to not post your printers serial number on our forums you can also contact us in tech support by submitting a request using the form at the bottom of this page: https://lulzbot.com/Support
Also, I apologize if this seems obvious, but after installing the new toolhead and flashing your firmware did you make sure to update the E-Steps on your printer to the value listed on the back of your Flexystruder and save the change once it had been made? The E-Steps control the overall rate of extrusion in correlation to the turns of the motor so if this wasn’t set to the correct value it could cause general extrusion difficulties.