Cestari,
On my 5 port, i use stock full 2047 GO Pipe, no need to change the header. You are going with a shorter one anyway, so that lack of bottom its kinda ok.
Go with this guys are telling you, stock shims and stock header and go to the track and test.
I dont know how are you repect to sea level, here in Santiago de Chile we are 543 meters over sea level, and i use the extra shim just for initial break inn (first gallon) and after that i run stock shims no extra one ...
My temps are 240-260 right now, great runtimes, great power too on low and high end ...
Hope this helps,
cya !!