40 frame with 39 transmission

I'd go with 40 pedals and use the 40 release linkage, including the relay shaft.

Mart.
 
If you have a 39 transmission with the 39 cross shaft arm it would probably make sense to use 39 pedals and linkage. If your transmission happens to have the 40 cross shaft it would make sense to use 40 pedals and 40 linkage. JMO
 
Assuming your 40 frame still has the bracket for the clutch equalizer shaft/lever, you would be better off staying with that set up. You can use the '40 pedal assy which is easier to find (and generally less expensive). The trans will need the 40-48 clutch release shaft of course.
 
Use whichever pedal setup you find first/cheapest. And get the shaft hardware to match. As Mac said, the '40 will be cheaper.
 
All I know is, when trying to refurb the 39 pedals in my 33, I could not get the large diameter bush for the brake pedal. 39 pedals are being reproduced now, I don't know if that will improve the availability of the bush.

Mart.
 
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