The 2nd gear jerkiness, is a standard for the shiftkit for a lot of people. It can be quite clunky.
The transmission is 'adaptive' and it will take a while to drive and for it to 'relearn'. Sadly when you clear the ecu etc it doesnt actually clear the tcm. I am unsure of anythign besides consult being able to clear the parameters also.
As for the rest of your sumptoms are you having any other issues? Only time ive had the dash dissapear is when my IPDM got wet, that also made the gearbox run full line pressure constantly.