Same i need to put the box in to get the angle correct, i cant fit the drivers side header either as hits the strut tower, think ill get the top pipe modified to hug the head more.
The instructions say the header has to go on before the motor is dropped in. At the same time, I discovered last week that I can get the header out through the bottom if I pull the manual steering box at the same time. As in, they have to both be loose and move kind of as a unit. Without a bellhousing, it would be even easier. But I really doubt the Borgenson box would work the same, but haven't tried it. Either way, sounds like you are trying to get them in after dropping the motor in and that probably won't work from the top.