[JM 35 Sedan]

I put Fenton's, purchased from Speedway 10 years ago, on my '35 traditional hotrod build that has a 59 294ci engine, '39 transmission, '37-'41 transmission mount bolted to frame, '37 steering box and '37-'41 steering box to frame mount.
I removed material from the flanges as you are talking about doing. I also removed a slight amount of material from the header surface that's nearest to the steering box. These headers do have thick walls. Then I removed a slight amount of material from that corner of the steering box that comes closest to the manifold. I believe I also milled the mounting surface of the steering box casting very lightly. Wound up with about 1/4" clearance without the need to put any additional shims/washers/spacers between rubber donut mounts and cast iron mounts on water pumps. Too much lift on the front of my '35 engine could put the generator mounted fan into the bottom of the large tank top radiator. I did use new rubber donut mounts, with a single flat washer that normally comes with these new rubber mounts, at the front of the engine and at the transmission to frame mounts.
This all worked well to give the clearance necessary, especially if you consider that the normal rotational inertia of the engine will tend to increase that space between the steering box and Fenton exhaust manifold.