Flathead header is totally different than a 5.0 header, sounds like you need to look at the various block huggers that are out there
It's unfortunate @Matt C. never came back so give feedback on the help he was given and how it panned out. That would be helpful.
With a small block Chevy in the '38 Ford pickup, I used a manual box out of a '64 Chevelle--not sure if that is the 525, but it came out of a wrecked Chevelle with only 11,000 miles on it. The cool thing about it is that the splines are the same as the orginal Ford box and the Ford pitman arm fits it. Steered easily. The trick on exhaust clearance was to use a passenger side exhaust manifold from a '67-'72 Chevy pickup on the driver's side.
My 39 had a 525 box when I bought it with a flathead. Absolute nightmare!!!! Replaced with a Vega box, its OK but not ideal . I am building a 40 coupe currently and am rebuilding the original box. This is the best way in my opinion. I wish my 39 still had the original box, it would be a much nicer driving car!!!
Naturally I have to ask why? I can't see the installation, but have to suspect there is something fundamentally off with what was done to cause such a negative outcome and****essment. The installation of a Vega box also causes a raised eyebrow. Also, when you say '525' and 'Vega', do you know who actually manufactured these? Between installation and parts, I'm looking for clues in the dark.
I have a 50 ford with flathead and cannot find parts to rebuild, suppliers advertise parts but are out of stock. What other box can i adapt to the 50?