Run hard tresh small wire concaves in front position, small wire regular in second, slotted in third and slotted or blank in forth. Also run a hard thresh cover in the return(has dimples on it to try to thresh out bolls that go through the return. I also tape up the return and clean grain doors as flax will leak out because they flex.
You need to run hard thresh concaves in the front two positions and not the case hard thresh because the wires are too far apart.In the the 3&4 position run small wire. Presieve closed and both top and bottom sieve at 5/16 and fan at 650rpm.
Lift spreaders up, disengage chopper and roll. I have always dropped it in a row and burn the rows. Have a 40' header though so it has more to keep rows burning. I have never plugged the chopper and it has always flowed through the hole with no problems.