Seems like it'd be easier to work with the motor plate to make your headers clear, then to have to re-work the headers to clear the motor plate. I don't know your setup, I may be way off in my thinking.
Lot of drag cars just use a cam spud drive, drives the pump off of the camshaft. Requires special front cover and a lot of times remote water pump. But it works slick. On a SBC it's simple but on a Ford, I haven't seen a lot of them. At one time, Ken Lowe had a setup to run a cam driven pump, but I don't remember if it was cleveland or windsor. MPG heads might have a cover too. RYR has one, that is set up for belt drive, but you can change the outer cover to run a mechanically driven pump off the cam.
I just mounted mine right on the motor plate, done. But I don't have forward facing headers either, so it was really easy.
'92GT, 427" and '93 "LXVO" coupe