seriously, header design discussion is an ENORMOUS topic and theres no simple answer. but yes, firing order is important with their design.
hmmmm, think ill just cut to the chase a recommend a basic workable header design for the 2jz:
6-2-1 collector design
cyls 1+2+3 in one group
cyls 4+5+6 in the other
primary tube internal dia of 1 5/8"
primary tube length of 25-28"
secondry tube internal dia of 2"
secondary tube length around 36-40"
final collector internal dia 2 1/2"